Biology subjects

Fernandez, J.

Publications and source records attributed to Fernandez, J..

At least 19 recordsLinked to original sources

bioRxiv2026

DNA damage at Lamina-Associated Domains triggers nuclear envelope reorganization and chromatin detachment to prevent nuclear envelope blebbing and genome instability.

The nuclear periphery anchors large, transcriptionally silent chromatin domains to the nuclear envelope and plays a central role in maintaining genome stability, acting as a dynamic hub for DNA repair. Nevertheless, how cells process DNA damage within lamina-associated domains (LADs), which reside in this environment, remains poorly understood, despite their relevance to nuclear architecture, aging, and senescence. By employing systems for temporally controlled and spatially precise induction of DNA double-strand breaks (DSBs) within LADs, we show that DSBs within LADs trigger remodeling of the nuclear lamina and the dynamic detachment of damaged LADs from the nuclear envelope, resulting in their relocalization to the nuclear interior. This process is orchestrated by the ATM/{gamma}H2AX/MDC1/RNF168/53BP1 axis and requires the linker of nucleoskeleton and cytoskeleton (LINC) complex and cytoskeletal components while leaving DNA repair pathway choice unchanged. Persistent tethering of damaged LADs at the nuclear periphery delays the DNA damage response and repair, elevates genomic instability, and drives chromatin extrusion through nuclear blebs directly linking failed repair to dysregulation of nuclear integrity. These findings reveal a protective mechanism in which ATM-driven LAD dynamics and nuclear envelope remodeling might relieve mechanical stress, facilitate repair, and safeguard both genome stability and nuclear architecture.

cell biology↗

bioRxiv2026

A Gnotobiotic Rice Pathosystem Reveals How the Microbiome Suppresses Rice Blast Disease

Rice blast disease caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae poses a major threat to global rice production, creating an urgent need for sustainable disease management strategies. Because plant-associated microbiomes can contribute to pathogen suppression and host defense, their role in rice blast resistance is of considerable interest. However, interactions among M. oryzae, rice, and the rice microbiome remain poorly understood. Using a gnotobiotic rice pathosystem, we investigated how microbiome colonization influences host responses to infection and how bacterial community structure changes following pathogen challenge. Microbiome colonization significantly reduced blast disease severity, while differential abundance analyses identified infection-associated shifts in bacterial community composition, including enrichment of Brevibacillus-associated taxa. Functional characterization of cultured endophytes revealed plant growth-promoting traits and antagonistic activity against M. oryzae. Two synthetic communities assembled from healthy- and infected-derived isolates significantly reduced disease severity, demonstrating that disease suppression can be recapitulated using simplified microbial communities. Interestingly, axenically grown plants exhibited elevated basal expression of multiple defense-associated genes but greater disease severity and reduced chitin-induced ROS production compared with holoxenic plants. In contrast, microbiome-colonized plants displayed enhanced ROS responsiveness and reduced disease, suggesting that the rice microbiome promotes a more effective and regulated immune state rather than simply increasing defense activation. Together, these findings advance our understanding of rice-microbiome-M. oryzae interactions and establish a tractable experimental platform for mechanistic studies of microbiome-mediated disease suppression.

microbiology↗

bioRxiv2026

Biochemical and Mechanistic Characterization of the DNA-dependent Poly(ADP-ribose) Polymerase, MoPARP1, in Magnaporthe oryzae

Poly(ADP-ribose) polymerases (PARPs) are important regulators of DNA repair and cellular stress responses in eukaryotes. Although mammalian PARPs have been extensively characterized, comparatively little is known about PARPs in pathogenic filamentous fungi. Here, we define biochemical features of MoPARP1 from the plant-pathogenic fungus Magnaporthe oryzae. Mutation of the conserved catalytic glutamate E714 abolished detectable PARylation activity, whereas PAR generated by MoPARP1 was hydrolyzed by human PARG, suggesting synthesis of polymeric ADP-ribose. Several mammalian PARP inhibitors were effective against MoPARP1 in vitro, consistent with conservation of the catalytic inhibitor-binding pocket. DNA substrates containing 5' phosphate enhanced MoPARP1 catalytic activity, while both wild-type MoPARP1 and the catalytically inactive MoPARP1 E714A bound diverse DNA substrates. Quantitative analyses revealed that structurally distinct DNA substrates exhibit similar apparent binding affinities yet yield markedly different catalytic outputs, suggesting that DNA engagement alone does not determine productive PAR synthesis. MoPARP1 lacks the canonical N-terminal zinc-finger domains of human PARP1 and instead depends on its WGR-containing region for DNA association. Domain truncation analyses showed the BRCT-WGR region supports high-affinity DNA binding, whereas the WGR-PARP region retains catalytic competence despite weaker DNA affinity. Together, these findings establish a mechanistic framework for DNA-dependent PARylation in a filamentous fungal plant pathogen.

biochemistry↗

bioRxiv2026

Pseudomonas effector AvrC is a rhamnosyltransferase with broad substrate specificity

Plant cells can directly or indirectly detect bacterial effectors, triggering a hypersensitive response to defend against pathogen infection. One extensively studied effector, AvrB, is a Fido (Fic, Doc, AvrB) domain-containing protein that acts as a glycosyltransferase. AvrC is an elusive Pseudomonas syringae avirulence effector protein with significant sequence and structural similarity to AvrB. Combining biochemistry, mass spectrometry, and AlphaFold prediction tools, we show that AvrC is a glycosyltransferase with auto-rhamnosylation activity. Like AvrB, AvrC can rhamnosylate a threonine residue (T166) on the A. thaliana guardee protein RIN4. In vitro assays revealed rhamnosylation substrates for AvrC also include plant coatomer subunits COPE1 and COPZ1. Collectively, our findings indicate that AvrC is a rhamnosyltransferase with broad substrate specificity. Our experimental strategies and findings provide valuable insights into future studies on the characterization of other Fido proteins.

biochemistry↗

bioRxiv2026

Soil-derived Bacillus pumilus strains demonstrate antagonistic activity against Magnaporthe oryzae and multiple plant growth-promoting traits

Biological control strategies are increasingly being explored as sustainable alternatives for managing rice blast disease caused by Magnaporthe oryzae. In this study, we characterized three Bacillus pumilus isolates (DC01, DC09, and DC13) and evaluated their antifungal and plant-beneficial properties against M. oryzae. Whole genome sequencing revealed multiple biosynthetic gene clusters associated with the production of antimicrobial metabolites. All three isolates inhibited fungal growth in dual-culture assays, whereas heat-stable diffusible antifungal activity was primarily associated with the cell-free supernatants of DC09 and DC13. Exposure to bacterial supernatants disrupted fungal development, inducing abnormal hyphal morphology characterized by bulbous swelling, altered polarity, and increased branching in M. oryzae. Volatile organic compound assays further revealed that the DC isolates suppress fungal growth in the absence of physical contact. The isolates additionally inhibited the growth of other phytopathogenic fungi and selected human bacterial pathogens. All strains exhibited plant growth-promoting traits, including indole-3-acetic acid production and osmotic stress tolerance, whereas DC09 also displayed phosphate-solubilizing activity. Importantly, root inoculation with the DC isolates significantly reduced rice blast disease severity and induced expression of defense-associated genes involved in jasmonic acid/ethylene signaling and immune priming. Collectively, these findings identify the DC isolates, particularly DC09 and DC13, as promising multi-mechanistic biological control agents for sustainable rice blast management.

microbiology↗

bioRxiv2025

Yeast as a platform to dissect poly(ADP-ribose) polymerase function from Magnaporthe oryzae and evaluate PARP inhibitors

Poly(ADP-ribose) polymerases (PARPs) regulate genome maintenance through NAD+-dependent ADP-ribosylation, yet PARP function in fungi remains poorly defined. Here, we reconstituted the activity of the Magnaporthe oryzae PARP1 homolog (MoPARP1) in Saccharomyces cerevisiae, a genetically tractable organism that lacks endogenous PARP enzymes. Galactose-induced expression of MoPARP1 reduced yeast growth, whereas a catalytically inactive mutant showed no defect, indicating that the growth phenotype depends on PARP catalytic activity. In a multidrug transporter-deficient background, the PARP inhibitor 3-aminobenzamide and the clinically used PARP inhibitor olaparib rescued the growth of MoPARP1-expressing strains, establishing a framework for inhibitor testing in vivo. Finally, MoPARP1-GFP localized to the nucleus independent of catalytic activity, supporting correct targeting in this heterologous system. Together, these findings establish yeast as a platform to dissect fungal PARP biology and evaluate chemical inhibition.

molecular biology↗

bioRxiv2025

Nutrient utilization and degradative enzyme activity of the dragon fruit canker pathogen, Neoscytalidium dimidiatum

Dragon fruit canker (DFC), caused by the pathogenic fungus Neoscytalidium dimidiatum, is a severe disease that threatens dragon fruit production worldwide. Current management efforts largely rely on fungicide applications and sanitation measures; however, the pathogens molecular genetic characterization, nutrient utilization preferences, and extracellular enzyme activities remain poorly understood. Using calcofluor white-based fluorescence microscopy, we demonstrate that nutrient limitation significantly restricts the growth and maturation of N. dimidiatum, impairing melanization and sporulation. Carbon utilization assays revealed a preference for maltose, suggesting reliance on starch-derived sugars. In addition, nitrogen utilization assays indicated efficient assimilation of complex organic nitrogen sources rich in peptides and amino acids. Finally, we experimentally validated extracellular enzymatic activities involved in host macromolecule degradation, including cellulase, amylase, pectinase, and protease activities. Collectively, these findings provide new insights into the physiology and pathogenic potential of N. dimidiatum and establish a foundation for developing improved strategies to mitigate DFC. Impact StatementNeoscytalidium dimidiatum is the causal agent of dragon fruit canker (DFC), one of the most devastating diseases affecting dragon fruit. Here, we investigated key features of N. dimidiatum biology relevant to disease development, including nutrient preferences and degradative enzyme activity. Our findings indicate that N. dimidiatum preferentially utilizes maltose as a carbon source, consistent with the use of starch-derived sugars, and grows efficiently on rich, complex organic nitrogen sources. Plate-based enzymatic assays aligned with these nutrient utilization patterns, revealing cellulase, amylase, pectinase, and protease activities. Collectively, this study provides new insights into N. dimidiatum physiology and establishes a foundation for future virulence studies that can ultimately support the development of improved DFC mitigation strategies.

microbiology↗

bioRxiv2025

The Global Wheat Full Semantic Organ Segmentation (GWFSS) dataset

Computer vision is increasingly used in farmers fields and agricultural experiments to quantify important traits. Imaging setups with a sub-millimetre ground sampling distance enable the detection and tracking of plant features, including size, shape, and colour. Although todays AI-driven foundation models segment almost any object in an image, they still fail for complex plant canopies. To improve model performance, the global wheat dataset consortium assembled a diverse set of images from experiments around the globe. After the head detection dataset (GWHD), the new dataset targets a full semantic segmentation (GWFSS) of wheat organs (leaves, stems and spikes) covering all developmental stages. Images were collected by 11 institutions using a wide range of imaging setups. Two datasets are provided: i) a set of 1096 diverse images in which all organs were labelled at the pixel level, and (ii) a dataset of 52,078 images without annotations available for additional training. The labelled set was used to train segmentation models based on DeepLabV3Plus and Segformer. Our Segformer model performed slightly better than DeepLabV3Plus with a mIOU for leaves and spikes of ca. 90%. However, the precision for stems with 54% was rather lower. The major advantages over published models are: i) the exclusion of weeds from the wheat canopy, ii) the detection of all wheat features including necrotic and senescent tissues and its separation from crop residues. This facilitates further development in classifying healthy vs. unhealthy tissue to address the increasing need for accurate quantification of senescence and diseases in wheat canopies.

plant biology↗

bioRxiv2025

Bacillus subtilis strain UD1022 as a biocontrol agent against Magnaporthe oryzae, the rice blast pathogen

Rice blast disease, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating sustainable disease management strategies. Compared to chemical pesticides, biocontrol agents, such as beneficial microbe antagonists, offer a sustainable approach to naturally inhibit plant pathogens. This study evaluates the biocontrol potential of Bacillus subtilis UD1022 against M. oryzae through both direct antagonism and volatile-mediated inhibition. In dual culture assays, UD1022 significantly inhibited fungal growth. Furthermore, a stacking plate assay demonstrated that UD1022 produces volatile organic compounds (VOCs) that suppress fungal growth. Beyond vegetative growth inhibition, UD1022 also disrupted key infection processes of M. oryzae. Spore germination was reduced by 50%, while appressorium formation decreased by approximately 44% in UD1022-treated samples. In planta assays revealed that UD1022-treated rice plants exhibited a substantial reduction in disease severity compared to untreated controls. This reduction correlated with the upregulation of key defense genes in the salicylic acid, jasmonic acid, and ethylene signaling pathways, suggesting that UD1022 primes systemic resistance in rice plants. These findings establish UD1022 as a potent biocontrol agent capable of suppressing M. oryzae through direct antagonism, VOC-mediated inhibition, and induction of systemic resistance. This study underscores the potential of UD1022 as an eco-friendly alternative to chemical fungicides for managing rice blast disease. IMPORTANCEMagnaporthe oryzae is a destructive fungal pathogen that causes rice blast disease, leading to significant yield losses and threatening global food security. Here, we investigated the biocontrol potential of Bacillus subtilis UD1022, a beneficial rhizobacterium known for its plant growth-promoting and antifungal properties. Our in vitro and in planta studies revealed that UD1022 suppresses M. oryzae through direct antagonism, volatile organic compound (VOC)-mediated inhibition, and the induction of systemic resistance in rice. These findings demonstrate UD1022 as a promising candidate for microbial-based disease management and the role of beneficial bacteria in enhancing crop protection. This research contributes to the development of sustainable agricultural practices by leveraging naturally occurring microbes to improve plant resilience and disease resistance.

microbiology↗

bioRxiv2025

LAVR-289, a new acyclo-nucleoside phosphonate having broad-spectrum activity against herpesviruses.

Human herpesviruses are latent opportunistic large dsDNA viruses that can have deleterious effect in immunocompromised patients by triggering life-threatening infections. Over the past years, different antivirals have been developed against a variety of herpesviruses, including Acyclovir for herpes simplex viruses (HSV1 and 2) and ganciclovir and letermovir for human cytomegalovirus (hCMV). However, broad-spectrum inhibitors of herpesvirus infections are still missing. Here we report the efficacy of LAVR-289, a new acyclic nucleoside analog, on a broad variety of herpesviruses from human and animal origin. LAVR-289 displays nanomolar efficiency in vitro, is active on viral strains resistant to gold standard antivirals and ex vivo on reconstituted human skin infected with HSV1. Combined with its anti-poxvirus and anti-adenovirus activity, LAVR-289 can become the next gold standard for the management of opportunistic virus infections in immunocompromised patient.

microbiology↗

bioRxiv2024

The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine

The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/or diet in humans. Following cellular uptake, Q is incorporated at the wobble base (position 34) of tRNAs with a GUN anticodon, which is important for efficient translation. Early studies suggested that cytosolic uptake of queuine is mediated by a selective transporter that is regulated by mitogenic signals, but the identity of this transporter has remained elusive. Here, through a cross-species bioinformatic search and genetic validation, we have identified the solute carrier family member SLC35F2 as a unique transporter for both queuine and queuosine in Schizosaccharomyces pombe and Trypanosoma brucei. Furthermore, gene disruption in HeLa cells revealed that SLC35F2 is the sole transporter for queuosine in HeLa cells (Km 174 nM) and a high-affinity transporter for the queuine nucleobase (Km 67 nM), with the presence of another low-affinity transporter (Km 259 nM) in these cells. Competition uptake studies show that SLC35F2 is not a general transporter for other canonical ribonucleobases or ribonucleosides, but selectively imports q and Q. The identification of SLC35F2, an oncogene, as the transporter of both q and Q advances our understanding of how intracellular levels of queuine and queuosine are regulated and how their deficiency contributes to a variety of pathophysiological conditions, including neurological disorders and cancer. Significance StatementThe discovery of SLC35F2 as the eukaryotic transporter of queuine and queuosine is key to understanding how these micronutrients are salvaged from the human gut and distributed to different body tissues. Queuosine modification of tRNAs enhances the accuracy and efficiency of codon-anticodon pairing and regulates a range of biological and pathophysiological states, including oxidative stress responses, cancer, learning, memory, and gut homeostasis.

biochemistry↗

bioRxiv2024

The Nuclear Pore Complex acts as a hub for pri-miRNA transcription and processing in plants

The regulation of miRNA biogenesis and movement is essential for plant development and environmental responses. HASTY (HST), a karyopherin protein, has been implicated in miRNA biogenesis and movement, though its role in non-cell-autonomous miRNA movement remains unclear. Through a genetic screen, we identified that mutations in the HAWAIIAN SKIRT (HWS) gene suppress the developmental defects of hst mutants by restoring miRNA movement. Our findings show that HWS interacts with nuclear transport factors and nuclear pore complex (NPC) components, including NUP1, positioning HWS as a regulator of miRNA nuclear export. Using microscopy and fluorescence in situ hybridization, we showed that pri-miRNA transcription, and likely their co-transcriptional processing, occurs at the nuclear pore. Notably, we uncovered an antagonistic relationship between HST and HWS in regulating MIRNA transcription at the NPC and AGO1 loading, which could explain the observed changes in miRNA movement. HST promotes the association of MIRNA loci with the NPC, likely facilitating co-transcriptional processing, while HWS negatively regulates this process by targeting MEDIATOR complex subunits to degradation detaching, consequently, the processing complex from the NPC. Furthermore, our data provides evidence of spatial coordination of miRNA transcription, biogenesis, and movement highlighting a novel role for the NPC in the miRNA pathway.

plant biology↗

bioRxiv2024

Interplay of Virulence Factors and Signaling Molecules: Albumin and Calcium-Mediated Biofilm Regulation in Bordetella bronchiseptica

Bordetella bronchiseptica, a respiratory pathogen capable of infecting various mammals, including humans, is associated with chronic infections, contrasting with the acute infections caused by Bordetella pertussis. Both pathogens can form biofilm-like structures in vivo, providing tolerance against environmental stresses. Biofilm formation by B. bronchiseptica is regulated by the BvgAS two-component system, with intermediate concentrations of certain modulators inducing a phase favoring biofilm formation. Recent studies have highlighted the role of cyclic diguanylate monophosphate (c-di-GMP) in this process: elevated c-di-GMP levels stimulate biofilm formation, whereas phosphodiesterase (PDE) activation reduces biofilms. Respiratory secretions, which contain albumin and calcium at higher concentrations than standard growth media, promote an increase in the amount and extracellular localization of the adenylate cyclase toxin (ACT), an important Bordetella spp. virulence factor. Secreted ACT present in the extracellular media or attached to the outer membrane inhibits biofilm formation. Based on these observations, we hypothesized that serum albumin and calcium together inhibit biofilm formation and explored the potential role of c-di-GMP in this process. Our findings demonstrate that serum albumin and calcium inhibit B. bronchiseptica biofilm formation by two apparently independent mechanisms, increasing AC secretion and inducing c-di-GMP degradation. This study contributes to the understanding of the mechanisms governing B. bronchiseptica biofilm formation and its modulation by host factors.

microbiology↗

bioRxiv2024

Metabolic vulnerabilities in Down syndrome B-cell acute lymphoblastic leukemia can be targeted using Venetoclax

Children with Down syndrome (DS) and B-cell acute lymphoblastic leukemia (B-ALL) are at increased risk for treatment-related mortality and relapse, highlighting the need for new therapies. Leukemia cell lines (CLs) have been fundamental to understanding therapeutic responses to pharmacological agents. We generated three DS B-ALL CLs characterized with diverse genomic alterations, including IGH::CRLF2 rearrangement (BCR::ABL1 like), mutations in FLT3 and TP53, and a novel ERG::CEBPD rearrangement. DS CLs had diminished proliferation, metabolism, and mitochondrial function when compared to non-DS (NDS) CLs and interestingly, these findings were similar to NDS Philadelphia chromosome-like (Ph-like) B-ALL CLs. Based on similar mitochondrial defects and prior preclinical data using Venetoclax for Ph-like B-ALL, we hypothesized that Venetoclax would be effective in DS. Intriguingly, Venetoclax was more effective in DS when compared to both NDS and Ph-like CLs. Efficacy was observed in DS patient derived xenografts (PDXs) and diagnostic/relapsed patient samples treated with Venetoclax, which synergized with Trametinib and Vincristine. Mass spectrometry-based multiomics analyses in DS and NDS B-ALL patient samples revealed an enriched metabolite profile in DS, particularly in the hubs of glucose metabolism and polyunsaturated phosphatidylcholines and phosphatidylinositols. Transcriptome analyses in DS B-ALL patients (n=249) supported enhanced glucose and fatty acid metabolism. Glucose regulated B-ALL viability through de novo serine biosynthesis. Targeting serine synergized with Venetoclax in DS B-ALL CLs. In summary, we have generated novel tools for studying DS B-ALL and identify altered metabolism in DS that responds to Venetoclax.

cancer biology↗

bioRxiv2024

A murine experimental model of the unique pulmonary thrombotic effect induced by the venom of the snake Bothrops lanceolatus

BackgroundThe venom of Bothrops lanceolatus, a viperid species endemic to the Lesser Antillean Island of Martinique, induces a unique clinical manifestation, i.e., thrombosis. Previous clinical observations indicate that thromboses are more common in patients bitten by juvenile specimens. There is a need to develop an experimental model of this effect in order to study the mechanisms involved. Methodology/principal findingsThe venoms of juvenile and adult specimens of B. lanceolatus were compared by (a) describing their proteome, (b) assessing their ability to induced thrombosis in a mouse model, and (c) evaluating their in vitro procoagulant activity and in vivo hemostasis alterations. Venom proteomes of juvenile and adult specimens were highly similar. When injected by the intraperitoneal (i.p.) route, the venom of juvenile specimens induced the formation of abundant thrombi in the pulmonary vasculature, whereas this effect was less frequent in the case of adult venom. Thrombosis was not abrogated by the metalloproteinase inhibitor Batimastat. Both venoms showed a weak in vitro procoagulant effect on citrated mouse plasma and bovine fibrinogen. When administered intravenously (i.v.) venoms did not affect classical clotting tests (prothrombin time and activated partial thromboplastin time) but caused a partial drop in fibrinogen concentration. The venom of juvenile specimens induced partial alterations in some rotational thromboelastometry parameters after i.v. injection. No alterations in coagulation tests were observed when venoms were administered i.p., but juvenile and adult venoms induced a marked thrombocytopenia. Conclusions/significanceAn experimental model of the thrombotic effect induced by B. lanceolatus venom was developed. This effect is more pronounced in the case of venom of juvenile specimens, despite the observation that juvenile and adult venom proteomes are similar. Adult and juvenile venoms do not induce a consumption coagulopathy characteristic of other Bothrops sp venoms. Both venoms induce a conspicuous thrombocytopenia. This experimental model reproduces the main clinical findings described in these envenomings and should be useful to understand the mechanisms of this thrombotic effect. Author summaryEnvenomings by the viperid species Bothrops lanceolatus, endemic of the Caribbean Island of Martinique, are characterized by a unique thrombotic effect responsible for infarcts in various organs. Until now, no experimental in vivo models of this effect have been described. In this study, we developed a mouse model of thrombosis by using the intraperitoneal route of venom injection. The venom of juvenile specimens of B. lanceolatus induced the formation of abundant thrombi in the lungs, whereas the effect was much less pronounced with the venom of adult specimens. This difference in the ability of juvenile and adult venoms occurs despite both venoms having highly similar proteomic profiles. Both adult and juvenile venoms showed a weak in vitro procoagulant effect on plasma and fibrinogen, underscoring a thrombin-like (pseudo-procoagulant) activity. In vivo, the venoms did not affect the classical clotting tests (prothrombin time and activated partial thromboplastin time) but induced a partial drop in fibrinogen concentration and limited alterations in rotational thromboelastometry parameters when injected by the i.v. route. In contrast, few alterations of these parameters were observed after i.p. injection of venoms, in conditions in which thrombosis occurred, hence evidencing the lack of a consumption coagulopathy. After i.p. injection both venoms induced a pronounced thrombocytopenia. This experimental model reproduces some of the main clinical manifestations of envenoming by this species. This model can be used to identify the toxins responsible for the thrombotic effect, to study the mechanism(s) of thrombosis and to assess the preclinical efficacy of antivenoms.

pharmacology and toxicology↗

bioRxiv2024

A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia

ASXL1 is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), alongside DNMT3A and TET2. CH can progress to myeloid malignancies including chronic monomyelocytic leukemia (CMML), and is also strongly associated with inflammatory cardiovascular disease and all-cause mortality in humans. DNMT3A and TET2 regulate DNA methylation and demethylation pathways respectively, and loss-of-function mutations in these genes reduce DNA methylation in heterochromatin, allowing de-repression of silenced elements in heterochromatin. In contrast, the mechanisms that connect mutant ASXL1 and CH are not yet fully understood. CH/CMML-associated ASXL1 mutations encode C-terminally truncated proteins that enhance the deubiquitinase activity of the ASXL-BAP1 "PR-DUB" deubiquitinase complex, which removes mono-ubiquitin from H2AK119Ub. Here we show that ASXL1 mutant proteins interact with the EHMT1-EHMT2 methyltransferase complex, which generates H3K9me1 and me2, the latter a repressive modification in constitutive heterochromatin. Compared to cells from age-matched wildtype mice, we found that expanded myeloid cells from old ([≥]18-month-old) Asxl1tm/+ mice, a heterozygous knock-in mouse model of CH, display genome-wide decreases of H3K9me2, H3K9me3 and H2AK119Ub as well as an associated increase in expression of transposable elements (TEs) and satellite repeats. Increased TE expression was also observed in monocytes from ASXL1-mutant CMML patients compared to monocytes from healthy controls. Our data suggest that mutant ASXL1 proteins compromise the integrity of both constitutive and facultative heterochromatin in an age-dependent manner, by reducing the levels of H3K9me2/3 and H2AK119Ub. This increase in TE expression correlated with increased expression of nearby genes, including many interferon-inducible (inflammation-associated) genes (ISGs). Significance StatementAge-related clonal hematopoiesis (CH) is a premalignant condition associated with inflammatory cardiovascular disease. ASXL1 mutations are very frequent in CH. We show that ASXL1 interacts with EHMT1 and EHMT2, H3K9 methyltransferases that deposit H3K9me1 and me2. Using a mouse model of mutant ASXL1 to recapitulate CH, we found that old ASXL1-mutant mice showed marked expansion of myeloid cells in bone marrow, with decreased H3K9me2/3 and increased expression of transposable elements (TEs) in heterochromatin. In humans, ASXL1-mutant CH progresses to chronic monomyelocytic leukemia (CMML); CMML patient samples showed striking upregulation of many TE families, suggesting that ASXL1 mutations compromise heterochromatin integrity, hence causing derepression of TEs. Targeting heterochromatin-associated proteins and TEs might counter the progression of CH, CMML and other myeloid malignancies.

cancer biology↗

bioRxiv2023

A polarized cell system amenable to subcellular resolution imaging of influenza virus infection

The life cycle of influenza A viruses (IAV), and notably intracellular trafficking of the viral genome, depend on multiple interactions with the cellular cytoskeleton and endomembrane system. A limitation of the conventional cellular models used for mechanistic study and subcellular imaging of IAV infection is that they are cultured in two dimensions (2D) under non-polarizing conditions, and therefore they do not recapitulate the intracellular organization of the polarized respiratory epithelial cells naturally targeted by IAVs. To overcome this limitation, we developed an IAV-infection assay in a 3D cell culture system which allows imaging along the baso-lateral axis of polarized cells, with subcellular resolution. Here we describe a protocol to grow polarized monolayers of Caco2-TC7 cells on static Cytodex-3 microcarrier beads, infect them with IAV, and subsequently perform immunostaining and confocal imaging, or electron microscopy, on polarized IAV-infected cells. This method can be extended to other pathogens that infect human polarized epithelial cells.

microbiology↗

bioRxiv2023

Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile

H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 - March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 - 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.

microbiology↗