Biology subjects

Deng, X.

Publications and source records attributed to Deng, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

MRN-ATM Pathway Activation in CD4 T-Cell Senescence during Chronic Hepatitis B Virus Infection

T-cell senescence is a hallmark of immune dysfunction in persistent viral infections, characterized by DNA damage accumulation and telomere erosion. However, the mechanisms driving CD4 T-cell senescence in the context of chronic hepatitis B virus (HBV) infection remain poorly defined. In this study, we demonstrated that people with chronic HBV infection exhibited CD4 T-cell senescence, marked by elevated KLRG1, along with increased DNA damage and telomere shortening, compared to HS. Notably, activation of the MRN-ATM (MRE11/RAD50/NBS1-Ataxia Telangiectasia Mutated Protein) pathway was prominent in CD4 T cells from HBV patients. Importantly, suppression of MRN attenuated ATM phosphorylation and its downstream signaling molecules, and inhibition of ATM reduced the production of proinflammatory cytokines in CD4 T cells derived from both HBV patients and HS. These results suggest that in chronic HBV infection, the virus induced CD4 T-cell senescence, telomere erosion, and DNA damage, while concurrent activation of the MRN-ATM pathway may serve as a compensatory mechanism to preserve CD4 T-cell function. Elucidating this relationship between T-cell senescence and DNA damage repair helps to understanding the mechanisms underlying HBV persistence and providing potential therapeutic targets against chronic HBV infection.

immunology↗

bioRxiv2026

A population-scale red blood cell proteome reveals genetically encoded aging clocks predictive of hemolysis and blood donor activity

As the most abundant human cell and the foundation of transfusion medicine, red blood cells (RBCs) offer a unique readout of systemic health, yet they have never been characterized at population scale. We generated a proteome atlas of 13,091 blood donors with multi-omics longitudinal phenotyping, characterizing the influence of demographics and genetic variation on the reproducibility of RBC proteomes across donations. Elastic-net aging clocks captured biological aging with high accuracy and uncovered genetic regulators of {Delta}Age at FN1, C4/IKZF1, CRAT, PFAS, TRIM58. Across independent cohorts, {Delta}Age was accelerated in G6PD deficiency, sickle cell trait/disease, and iron deficiency, reversed by iron repletion, and slowed in high-frequency donors, linking molecular aging to brain iron/myelin and cognitive performance. Molecular aging signatures predicted storage, osmotic, and oxidative hemolysis, hemoglobin increments after transfusion, and long-term donor activity over 12-years. These results establish RBC proteomics as a scalable biomarker of aging, donor healthspan, and transfusion outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/710284v1_ufig1.gif" ALT="Figure 1"> View larger version (96K): org.highwire.dtl.DTLVardef@15bd46eorg.highwire.dtl.DTLVardef@1d7c107org.highwire.dtl.DTLVardef@1c1d870org.highwire.dtl.DTLVardef@168dc6f_HPS_FORMAT_FIGEXP M_FIG Dzieciatkowska et al. generate the first population-scale atlas of the RBC proteome across 13,000 donors and develop proteomic and metabolomic aging clocks that quantify biological age. Molecular {Delta}Age is reproducible across donations, genetically encoded and accelerated in G6PD deficiency, sickle cell trait/disease, and iron deficiency - yet reset by iron repletion, tracking with cognitive function and brain iron/myelin. RBC aging clocks predict hemolytic fragility, transfusion efficacy, and donor activity 12 years later. C_FIG HighlightsO_LIRBC proteome atlas of 13,091 donors reveals demographic and genetic programs C_LIO_LIGenetically encoded RBC aging clocks identify regulators of molecular {Delta}age C_LIO_LIMolecular aging features predict hemolysis and transfusion response across cohorts C_LIO_LIRBC molecular age forecasts long-term donor activity over a 12-year follow-up C_LI

biochemistry↗

bioRxiv2026

MtDNA heteroplasmy controls tumor immune reprogramming through mitochondrial translation

Mitochondrial DNA (mtDNA) mutations are among the most frequent genetic alterations in human cancers, yet their molecular mechanisms in shaping tumor progression and metastasis under physiological conditions remain poorly understood. Here, we show that mtDNA heteroplasmy acts as a tumor cell-intrinsic rheostat that orchestrates fate decisions between progression and suppression. Moderate heteroplasmy induces a ribosomal storm of mitochondrial translation and ribosome biogenesis, driven by leucyl-tRNA synthetase 2 (LARS2). This response enhances metabolic fitness and licenses the secretion of S100A8/A9, enabling tumor cells to actively remodel the immune microenvironment through recruitment of myeloid-derived suppressor cells and exclusion of CD8 T cells, thereby promoting immune evasion and metastatic progression. In contrast, high heteroplasmy impairs tumorigenesis due to oxidative phosphorylation collapse. Disruption of LARS2, mitochondrial translation, or S100A9 signalling abrogates tumor progression. Our findings establish mtDNA heteroplasmy as a key regulator of cancer evolution, linking mitochondrial genetic variation to immune modulation, and reveal the LARS2-mitochondrial translation-S100A8/A9 axis as a therapeutically targetable programme within the pro-tumorigenic window of mtDNA heteroplasmy.

cancer biology↗

bioRxiv2026

Glucose is a ligand-like trigger for secretion of postprandial GLP-1

Glucagon-like peptide 1 (GLP-1) is secreted from the intestinal L cells in a glucose-dependent manner. However, the mechanism underlying how glucose stimulates the secretion remains unclear. Here, we found that glucose at postprandial concentrations near the Km of GK for glucose ([~]10 mM), as well as nonmetabolizable glucose analogs, triggers GLP-1 secretion by intestinal L cells through directly binding to glucokinase (GK), without increasing intracellular ATP levels. We also show that in postprandially high glucose, glucose-bound GK interacts and inhibits KATP, as assessed by immunoprecipitation and FRET-FLIM analyses, as well as patch clamping. In addition, we have utilized GK mutants identified in diabetics, demonstrating that those mutants defective in binding to glucose impair GLP-1 secretion in however high glucose, whereas mutants constitutively bound to glucose with defects in catalysis, promote GLP-1 secretion even in low glucose. Furthermore, the KATP mutant unable to bind to GK blocks GLP-1 secretion in high glucose. We have also provided evidence showing that sodium-glucose cotransporter 1 (SGLT1) plays an important role in the basal secretion of GLP-1, but not in high glucose. We have thus revealed that glucose the molecule itself and GK act as a ligand and the receptor, respectively, to induce GLP-1 secretion in response to high glucose, providing new therapeutic avenues targeting metabolic diseases.

biochemistry↗

bioRxiv2025

Blocking Minor Intron Splicing Disrupts DNA Repair and Overcomes Therapy Resistance in Prostate and Breast Cancer

The minor spliceosome (MiS) is a specialized RNA-processing machinery upregulated in cancer, promoting oncogene expression. We uncovered an adaptive resistance mechanism driven by secretion of extracellular vesicles enriched in U6atac snRNA, which amplifies MiS activity and promotes therapy resistance. Here, we show that U6atac snRNA, a crucial MiS component, reverses this process when depleted, revealing it as a druggable vulnerability in therapy-resistant prostate and breast cancers. U6atac knockdown triggers R-loop-mediated DNA damage while impairing repair by downregulating key DNA repair factors, disabling both homologous recombination and non-homologous end joining. This dual effect sensitizes prostate and breast tumors to PARP inhibitors, cisplatin, and radiation, independent of BRCA status. Across multiple in vitro and in vivo models, MiS targeting demonstrates tumor-selective activity with minimal toxicity. These findings position U6atac as a central regulator of genome stability and establish MiS targeting as a promising approach to potentiate genotoxic therapy and overcome resistance. Statement of significanceU6atac, a minor spliceosome component, is a crucial regulator of genome stability in cancer. Its knockdown triggers R-loop-driven DNA damage, downregulates DNA repair genes, and sensitizes tumors to DNA-damaging therapies while simultaneously blocking resistance mechanisms. Thus, minor spliceosome knockdown is a tumour-selective and broadly applicable therapeutic strategy.

cancer biology↗

bioRxiv2025

Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, the most common human enzymopathy, affects 6% of the global population, yet its impact on blood storage and transfusion efficacy remains undefined. We integrated genome-metabolome-proteome analyses of 13,091 blood donors (362 G6PD SNPs), validated in a recalled cohort (n=643), linked donor-recipient databases, humanized mouse models (canonical, African A- [V68M+N126D], Mediterranean [S188F]), and a prospective sickle cell disease study. Common G6PD variants reduced protein abundance, reprogrammed redox metabolism, and increased storage hemolysis. In mice, G6PD-deficient RBCs showed lower post-transfusion recovery, higher oxidative stress, and impaired renal oxygenation. Clinically, recipients of G6PD-deficient units exhibited smaller hemoglobin increments and reduced RBC L{superscript 1}Cr-survival (-8% at 24 h; -12% at 4 weeks). Structural studies revealed kinetic fragility for A- and thermodynamic fragility for Med-, linking genotype to protein instability and transfusion outcome. These findings identify donor G6PD genotype as a determinant of transfusion efficacy, supporting genotype-aware inventory-management strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/689741v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@1897489org.highwire.dtl.DTLVardef@1420587org.highwire.dtl.DTLVardef@178e8ddorg.highwire.dtl.DTLVardef@1003b44_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

The Critical and Unexpected Role of a Methyl Group in Interleukin-17A Inhibitors

Interleukin-17 (IL-17) is a pro-inflammatory cytokine primarily secreted by Th17 cells. It plays a crucial role in the bodys immune defense against fungal and bacterial pathogens. However, an imbalance in IL-17 production can contribute to the development of autoimmune and inflammatory disorders. Therapeutic strategies targeting IL-17, such as blocking antibodies like secukinumab (Cosentyx), have been successfully developed. These antibodies are currently employed in the treatment of various conditions, including psoriasis, psoriatic arthritis, and ankylosing spondylitis. More recently, a small molecule inhibitor of IL-17, LY3509754, progressed to clinical trials but was halted during Phase 1 due to unfavorable hepatotoxicity. Two derivatives, compounds 7 and 8, did not advance to clinical trials due to safety concerns. These three compounds (7, 8, and the original lead compound, presumably implied) share a common difluoro substituent, which was hypothesized to be the cause of the observed safety issues. In subsequent structure-activity relationship (SAR) studies, replacing the difluoro substituent with a single methyl group (resulting in compound 9) unexpectedly led to a significant improvement in cellular activity. Furthermore, compound 9 exhibited a very low unbound fraction and reduced liver distribution, ultimately translating to high in vivo efficacy with a sufficient safety margin. This seemingly minor methyl substitution transformed the compound into a highly promising preclinical candidate (compound 9), now slated for further development. Co-development inquiries are welcome. Please contact us at enan1@dcpc.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/680113v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@3f31adorg.highwire.dtl.DTLVardef@d6873forg.highwire.dtl.DTLVardef@494af7org.highwire.dtl.DTLVardef@1d8b7eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Viral evolution during primary infection in immunocompromised hosts

The immune response to viral infection is a delicate balance. By perturbing this balance, immunodeficiencies are expected to influence within-host viral evolution. Indeed, the presence of immunocompromised hosts has been argued to be a source of novel viral variants in some infectious diseases, including SARS-CoV-2. However, these arguments rest upon between-host models and so the role of immunodeficiencies on within-host evolution in primary infections is poorly understood. Using a mechanistic immunological model, here we consider how different immunodeficiencies shape the orchestration of the immune response during primary infection. We study how this alters the viral fitness landscape, thus speeding and slowing viral evolution. We show that during acute infections, while immunodeficiencies in neutrophils and interferon initially speed viral evolution, by the time the infection is cleared, mutations are at lower frequencies than in immunocompetent hosts. In persistent infections, we show that while T cell deficiencies slow viral evolution, interleukin-6 and macrophage deficiencies speed viral evolution. Finally, we show that positive epistatic interactions arising due to the immunological response will accelerate the evolution of viral mutations affecting the ability of virions to evade different aspects of the immune response and to enter host cells.

immunology↗

bioRxiv2025

Spen and Nito prevent dedifferentiation of progenitors by translationally repressing E(Spl)mγ

Rapid termination of Notch signaling by asymmetrically segregated Numb is essential for specification of differentiating progeny during asymmetric stem cell division. Using Drosophila type II neuroblasts as a model, here we report that specification of the differentiating progeny also requires the expression of the Notch target E(Spl)m{gamma} in the stem cell to be kept at low levels by the SPEN family proteins, Spen and Nito. We show that loss of Spen or Nito leads to a drastic increase in E(Spl)m{gamma} expression in the stem cell and subsequent dedifferentiation of its progeny. Genetic and biochemical studies demonstrate that Spen and Nito maintain the expression of E(Spl)m{gamma} in the stem cell at low levels by directly binding to two identical novel motifs in the 5UTR to repress its translation. The low expression in the stem cell prevents excessive inheritance of E(Spl)m{gamma} proteins by the differentiating progeny and ensures its rapid removal from the progeny. Together, our work uncovers a novel post-transcriptional mechanism regulating Notch signaling that is critical for cell fate specification during asymmetric stem cell division.

developmental biology↗

bioRxiv2025

Liquid-Liquid Phase Separation of Sp100-HMG: Driving Biogenesis and Functional Diversity of PML Nuclear Bodies

Promyelocytic leukemia nuclear bodies (PML NBs) are membraneless organelles (0.1-1 m) integral to fundamental cellular processes, yet the molecular logic governing their hierarchical organization is unclear. Contrary to the classical "PML-sole-scaffold" model, we identify Sp100-HMG as the unique isoform that autonomously nucleates into liquid-like condensates. Our findings establish an "inside-out" assembly paradigm, where Sp100-HMG initiates a liquid core that recruits PML and other client proteins (DAXX, ATRX) through three distinct cooperative processes: I. Multimerization domain- and intrinsically disordered region (IDR)-mediated LLPS of Sp100-HMG, nucleating the core; II. C-terminal-dependent protein-protein interactions enriching client components; and III. SUMOylation-directed PML recruitment, facilitating the formation of a stabilizing peripheral shell. This assembly paradigm extends beyond Sp100-HMG, as evidenced by ZBTB16--a PML NB-associated oncoprotein implicated in acute promyelocytic leukemia -- adopting an analogous mechanism to organize PML-positive condensates. Using HEp-2 cells as a main model, we show this hierarchical assembly is critical for orchestrating transcriptional programs and cell-cycle dynamics. Together, our study defines a new biogenesis mode for PML-NBs, where a master liquid nucleator coordinates shell integrity and plasticity for nuclear homeostasis. Significance StatementPML nuclear bodies (PML NBs) serve as essential organizers of the cell nucleus, yet the assembly principles underlying their biogenesis and linking it to functional heterogeneity, spatial positioning, and compositional diversity remain elusive. This study overturns the long-standing "PML-centric" view by establishing an LLPS-driven, hierarchical "inside-out" assembly paradigm. We identify Sp100-HMG as a master liquid nucleator that initiates a core to organize the outer PML shell. This inner-core LLPS-driven assembly logic is shared by other PML NB-associated factors, such as the oncoprotein ZBTB16, providing a unified biophysical framework to explain the structural integrity and plasticity of nuclear condensates. Functionally, this organizational process is critical for shaping the compositional diversity and spatial specificity of PML bodies, thereby modulating transcriptional programs and cell-cycle dynamics in a context-dependent manner. These findings offer broad insights into how organized protein condensation sustains nuclear homeostasis and its dysfunction in diseases such as leukemia.

cell biology↗

bioRxiv2025

Caffeine Impairs Red Blood Cell Storage Quality by Dual Inhibition of ADORA2b Signaling and G6PD Activity

Caffeine is the most widely consumed psychoactive substance globally, yet its peripheral physiological effects remain incompletely understood. Leveraging comprehensive data from 13,091 blood donors in the REDS RBC-Omics study, we identify caffeine as a significant modulator of red blood cell (RBC) storage quality and transfusion outcomes. Elevated caffeine levels were reproducible across multiple donations from 643 recalled donors, selected based on their extremes in hemolytic propensity. Both in the screening and recalled cohorts, higher caffeine levels were associated with disrupted RBC metabolism, characterized by reduced glycolysis, depletion of adenylate pools or 2,3-bisphosphoglycerate, and increased markers of oxidative stress and osmotic fragility, including kynurenine accumulation. These observations were recapitulated in plasma and RBCs of eight volunteers upon consumption of a cup of coffee independently of brewing method (Chemex vs espresso). Clinically, elevated caffeine correlated with increased hemolysis and lower post-transfusion hemoglobin increments, especially pronounced in recipients transfused with RBCs from donors carrying common polymorphisms in the ADORA2b gene, a key regulator of RBC metabolism in hypoxia. These human findings were mechanistically validated using a murine model deficient in ADORA2b, which demonstrated impaired glycolytic flux, compromised antioxidant defenses - including caffeine-dependent direct inhibition of recombinantly-expressed glucose 6-phosphate dehydrogenase, and decreased transfusion efficacy (lower hemoglobin increments, higher bilirubin post-transfusion), effects further exacerbated by caffeine exposure during storage. Our study positions caffeine consumption as a modifiable factor in blood transfusion practice, advocating for precision strategies that integrate genetic and exposome factors, and identifies metabolic interventions to enhance blood quality and clinical outcomes. One sentence summaryCaffeine consumption and genetic variants in the ADORA2b receptor synergistically impair red blood cell metabolism and transfusion efficacy, revealing a modifiable exposome-gene interaction for precision transfusion medicine.

biochemistry↗

bioRxiv2025

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species

Pseudouridine ({Psi}) modifications are the most abundant RNA modifications; however, their distribution and functional significance in bacteria remain largely unexplored compared to eukaryotic systems. In this study, we present the first transcriptome-wide and quantitative mapping of {Psi} modifications across five diverse bacterial species (Bacillus cereus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Pseudomonas syringae) at single-base resolution, utilizing the optimized BID-seq method for bacterial RNA. Our analysis revealed growth phase-dependent dynamics of pseudouridylation in bacterial tRNA and mRNA, particularly in genes enriched in core metabolic pathways. Comparative analysis demonstrated evolutionarily conserved features of {Psi} modifications, such as dominant motif contexts, {Psi} clustering within operons, etc. Functional analysis indicated {Psi} modifications influence bacterial mRNA stability, translation, and interactions with specific RNA-binding proteins (RBPs) in response to changing cellular demands during growth phase transitions. The integrated computational analysis on local RNA architecture was conducted to elucidate the structure-dependent {Psi} modifications in bacterial RNA. Furthermore, we developed an integrated deep learning framework, combining Transformer-GNN-based neural networks (pseU_NN) to capture both RNA sequence and structural features for effective prediction of {Psi}-modified sites. Overall, our study provides valuable insights into the landscapes of bacterial RNA {Psi} modifications and establishes a foundation for future mechanistic investigations into the functions of {Psi} in bacterial RNA regulation.

microbiology↗

bioRxiv2025

TMEDs Mediate Versatile Cargo Transport in Vesicle-dependent Unconventional Secretion

Unconventional protein secretion (UcPS) exports diverse signal peptide-lacking cargoes, yet its cargo selectivity remains poorly understood. Here, we identify TMED proteins as key regulators of vesicle-dependent UcPS, mediating selective cargo release via translocation into secretory carriers. TMED proteins act as translocators, facilitating cargo passage across lipid bilayers with assistance from HSP90 chaperones and partial cargo unfolding. Selectivity arises during translocation, where TMED cytoplasmic tails bind specific cargoes. The ER-Golgi intermediate compartment (ERGIC) is essential for TMED-mediated translocation and release. TMED homo-oligomerization enhances translocation, while hetero-tetramerization inhibits it. ERGIC localization promotes homo-oligomerization, which is further stabilized by cargo binding, forming a feed-forward mechanism to enhance translocation. These findings establish TMED proteins as central regulators of cargo diversity in UcPS, with their oligomerization and subcellular localization modulating translocation efficiency.

cell biology↗

bioRxiv2025

Discovery of D2469079A, A novel selective Toll-Like Receptor 7/8 Antagonist with Brain Penetrance

Aberrant activation of endosomal Toll-like receptors (TLRs) 7 and 8, which recognize single-stranded RNA, is strongly implicated in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). And the frequent neuropsychiatric involvement in SLE highlights the need for brain-penetrant therapies. Here, we report the identification and characterization of D2469079A, a novel, potent dual TLR7/TLR8 antagonist (low nM IC50 in humanized HEK-Blue assays) selective against hTLR9. D2469079A demonstrates favorable in vitro properties, including adequate solubility and high microsomal stability. It exhibited desirable pharmacokinetic profiles across multiple preclinical species (mice, rats, dogs) and achieved significant cerebrospinal fluid (CSF) exposure, confirming its high permeability and brain penetration. Consistent in vivo efficacy was observed in both acute and chronic stimulation models. Importantly, D2469079A displayed a favorable safety profile, lacking significant liabilities related to CYP450 inhibition/induction, hERG interaction, or toxicity in a 14-day rat study. These findings position D2469079A as a promising drug candidate with excellent drug-like characteristics for the treatment of TLR7/8-driven autoimmune diseases, potentially including neuropsychiatric manifestations. We are actively seeking partners for collaborative clinical development.

immunology↗

bioRxiv2025

Mutations differentially affecting the coronavirus Mac1 ADP-ribose binding and hydrolysis activities indicate that it promotes multiple stages of the viral replication cycle

All coronaviruses (CoVs) encode a conserved macrodomain, termed Mac1, in non-structural protein 3 (nsp3) that binds and hydrolyzes ADP-ribose covalently attached to proteins. Mac1 is a key virulence factor that counters antiviral ADP-ribosyltransferase (PARP) activity. Previously, we found that MHV strain JHM (JHMV) with a mutation in the adenine binding site, JHMV-D1329A, was extremely attenuated in all tested cell types as opposed to JHMV-N1347A, which only has a replication defect in bone-marrow derived macrophages (BMDMs). Interestingly, an N1347A/D1329A double mutant was unrecoverable, indicating an essential role for Mac1 in JHMV infection. We hypothesized that these mutations may impact different stages of the MHV lifecycle. First, to clarify how these mutations affected the biochemical activities of Mac1, we generated Mac1 proteins encoding the same mutations. As expected, the D-A mutation was extremely defective in ADP-ribose binding but maintained enzyme activity. In contrast, we previously found that the N-A mutation had WT levels of ADP-ribose binding but low enzyme activity, confirming that these mutations differentially effect the biochemical functions of Mac1. Following infection, D1329A displayed a large defect in the accumulation of viral RNA compared to WT or N1347A in all cells tested. Alternatively, N1347A infection produced normal levels of viral RNA but produced reduced levels of viral protein in interferon competent bone-marrow derived macrophages (BMDMs). These results suggest that Mac1 ADP-ribose binding and enzymatic activities promote different stages of the viral lifecycle, demonstrating the critical importance of Mac1 for JHMV replication. IMPORTANCEOver the last three decades, coronaviruses have repeatedly demonstrated their potential to become significant veterinary and public health threats. Zoonotic transmission of the myriad known coronavirus strains will remain a concern, regardless of the advances in vaccines and treatment. One difficulty in anticipating the next coronavirus outbreak is their diverse lineage and high propensity for mutation and recombination. The coronavirus macrodomain, Mac1, is conserved amongst all known coronaviruses and is also conserved in the Togaviridae and Hepeviridae families. Mac1 is a key factor in viral replication and pathogenesis, but its role in the replication cycle remains unclear. A deeper investigation of Mac1 function will identify conserved antiviral mechanisms and aid in the development of Mac1 inhibitors that represent a novel strategy for antiviral therapeutics.

microbiology↗

bioRxiv2025

Genetic architecture of the S-locus supergene revealed in a tetraploid distylous species

SummaryO_LIHeterostyly is a polymorphic floral adaptation controlled by supergenes and maintained in populations by disassortative mating. The molecular basis of distyly has been investigated in several unrelated families. Previous studies have been limited to diploid species and have not included Rubiaceae, which has the highest number of heterostylous species. C_LIO_LIHere, we investigate the genetic architecture of tetraploid Schizomussaenda henryi (Rubiaceae) to identify candidate style-length genes, evidence for hemizygosity and the potential role of gene duplication in the evolution of the S-locus. Chromosome-level genome assemblies and transcriptomic approaches identified the S-locus region comprised of four hemizygous genes. C_LIO_LIThe candidate gene SchzAUX22 may regulate style length and filament growth by acting in the auxin signaling pathway. Comparative studies of the two sub-genomes of S. henryi indicated strong similarities and no significant sub-genome dominance, as expected from autotetraploidy. Evidence from haplotype-resolved assemblies of a short-styled plant indicated that it possessed the ssSS genotype, consistent with autotetraploidy, which was estimated to have originated [~]3.6 Mya. Analysis of Ks values between S-locus genes and their paralogs indicated that the S-locus likely originated through stepwise duplication. C_LIO_LIOur study provides comprehensive genomic analysis of distyly in a polyploid and demonstrates that despite whole genome doubling the S-locus supergene remains intact and functional as an outbreeding mechanism. Our results contrast with many other heterostylous lineages where polyploidy is associated with breakdown of the polymorphism and transitions to self-fertilization. C_LI

plant biology↗

bioRxiv2025

Re: Concerns Regarding the Validation of ZYS-1 as a Bona Fide ADAR1 Inhibitor

Wang et al. in Nature Cancer report ZYS-1 as an ADAR1 inhibitor and present biochemical and cellular evidence to support ZYS-1s direct interaction with and inhibition of ADAR1, including enzymatic assays, surface plasmon resonance (SPR), drug affinity responsive target stability (DARTS), and cellular thermal shift assays (CETSA). We raise critical methodological concerns regarding the validation of ZYS-1 as a bona fide ADAR1 inhibitor. Our primary concern relates to the misuse of an adenosine deaminase (ADA) activity assay kit for ADAR1 enzymatic activity characterization. Using established biochemical assays with direct inosine quantification, we evaluated ZYS-1s inhibitory activity against ADAR1 using physiologically relevant RNA substrates. The compound showed no inhibitory activity at concentrations up to 1 mM. We demonstrate that the ADA assay kit used by Wang et al. does not reflect ADAR1-specific activity, and ZYS-1 is unable to inhibit ADAR1 in well-validated biochemical assays. We urge for further validation using ADAR1-specific assays to establish ZYS-1 as a genuine ADAR1 inhibitor.

pharmacology and toxicology↗

bioRxiv2025

Tubulin Regulates the Stability and Localization of STMN2 by Binding Preferentially to Its Soluble Form

Loss of the tubulin-binding protein STMN2 is implicated in amyotrophic lateral sclerosis (ALS) but how it protects neurons is not known. STMN2 is known to turn over rapidly and accumulate at axotomy sites. We confirmed fast turnover of STMN2 in U2OS cells and iPSC-derived neurons and showed that degradation occurs mainly by the ubiquitin-proteasome system. The membrane targeting N-terminal domain of STMN2 promoted fast turnover, whereas its tubulin binding stathmin-like domain (SLD) promoted stabilization. Proximity labeling and imaging showed that STMN2 localizes to trans-Golgi network membranes and that tubulin binding reduces this localization. Pull-down assays showed that tubulin prefers to bind to soluble over membrane-bound STMN2. Our data suggest that STMN2 interconverts between a soluble form that is rapidly degraded unless bound to tubulin and a membrane-bound form that does not bind tubulin. We propose that STMN2 is sequestered and stabilized by tubulin binding, while its neuroprotective function depends on an unknown molecular activity of its membrane-bound form.

cell biology↗