Biology subjects

Paul, S.

Publications and source records attributed to Paul, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Enhancement of low-temperature growth of Staphylococcus aureus by low concentrations of antimicrobial unsaturated fatty acids

The incorporation of oleic acid, a physiologically relevant and relatively non-toxic fatty acid, into membrane phospholipids and glycolipids has major impacts on the membrane biophysical properties of Staphylococcus aureus, including the promotion of low-temperature growth. Inclusion of oleic acid in growth media decreased the minimum growth temperature of S. aureus. It has not been studied yet whether other physiologically relevant, yet more antimicrobial straight-chain unsaturated fatty acids (SCUFAs), elicit similar responses. Here, we report that exogenous addition of these antimicrobial SCUFAs at 12{degrees}C led to their incorporation into the membrane lipids in only relatively small amounts, which, however, was sufficient to strongly promote growth at low temperatures. Intriguingly, these SCUFAs showed a preferential incorporation into diglucosyldiacylglyceride (DGDG) over phosphatidyl glycerol, and increased DGDG levels [~] 4-fold in SCUFA-grown S. aureus. Two glycolipid-deficient mutants lost the growth-enhancing effects of SCUFAs at low temperatures and showed increased susceptibility to SCUFAs at 37{degrees}C, suggesting that glycolipids are important membrane components and are required for low-temperature adaptation. The presence of SCUFAs at low temperatures also enhanced the production of the carotenoid staphyloxanthin. Overall, our results suggest that multiple strategies are at play in the membrane lipid remodeling of S. aureus to adapt to the stress of low-temperature growth and likely to other environmental stresses. Incorporation of antimicrobial SCUFAs into membrane lipids may facilitate the insertion of free forms of these SCUFAs into the membrane and be a part of their mode of action.

microbiology↗

bioRxiv2026

Sphingomyelin-Cholesterol Synergy as a Lipid Chaperone Driving Cytolysin A Pore Formation

Bacterial pathogens rely on pore-forming toxins (PFTs) to breach host barriers, a feat that requires water-soluble monomers to spontaneously metamorphose into membrane-inserted pores. In the extracellular milieu, these toxins must navigate complex folding landscapes without ATP-dependent chaperones. Here, we show that the synergistic interplay of host sphingomyelin (SM) and cholesterol (CHOL) acts as an intrinsic "lipid chaperone" that drives the conformational maturation of the bacterial toxin Cytolysin A (ClyA). Using leakage assays on vesicles and suspended lipid bilayer (SuLBs) arrays, atomistic molecular dynamics (MD) simulations, cell membrane permeabilization assays and biophysical measurements, we demonstrate that SM-CHOL synergy accelerates the rate-limiting unfolding of the toxins membrane bound {beta}-tongue motif into a reactive "molten globule" intermediate and guides its subsequent refolding into functional -helical conformation crucial for pore formation. We identify conserved lysine residues (K175 and K206) as critical molecular sensors that detect this specific lipid signature to drive productive transformation. This assembly process reciprocally remodels the host membrane and dismantling liquid-ordered domains, suggesting a mechanical coupling between toxin folding and the disruption of host lipid homeostasis. Our findings establish a paradigm of lipid-mediated chaperoning, revealing how pathogens co-evolve to exploit host lipid complexity to overcome the energetic barriers of membrane insertion.

biophysics↗

bioRxiv2026

Mettl3-catalyzed m6A methylation determines CD8+ T cell differentiation fate in tumor

The heterogeneity in patient responses to immune checkpoint blockade (ICB) is dictated by the relative abundance of exhausted CD8 T cell (Tex) subsets with distinct therapeutic responsiveness. Progenitor exhausted (pTex) cells remain sensitive to ICB, whereas terminally exhausted (tTex) cells are refractory; however, the molecular cues that bias differentiation toward these divergent fates remain poorly defined. Here, we identify the RNA methyltransferase Mettl3 as a central regulator of Tex fate. Across murine tumor models, human T cells, and adoptive transfer systems, Mettl3 expression is selectively enriched in tTex cells and inversely correlated with TCF1 pTex populations. Mechanistically, Mettl3 drives terminal exhaustion by stabilizing DNMT3B transcripts via mA modification, enforcing CpG methylation and chromatin compaction at memory-associated loci. Inhibition of the Mettl3-Dnmt3b axis reprograms chromatin accessibility toward memory-like states, thereby preserving progenitor potential and effector function. Consequently, T cells lacking Mettl3-Dnmt3b activity persist longer, mount robust recall responses, and achieve superior tumor control with enhanced responsiveness to PD-1 blockade. These findings establish the Mettl3-mA-Dnmt3b axis as a molecular rheostat of CD8 T cell fate, coupling epitranscriptomic regulation to epigenetic remodeling, and reveal a tractable pathway to improve the durability of cancer immunotherapy.

immunology↗

bioRxiv2025

PI3Kdelta promotes T cell effector differentiation and plasticity during chronic infection

Persistent antigen exposure in chronic infections and cancer leads to a progressive state of T cell dysfunction known as exhaustion, which represents a major barrier to effective immune control, but allows antigen-specific T cells to persist. Understanding signaling pathways that mitigate exhaustion and reinvigorate CD8+ T cell effector function is a key goal for immunotherapeutic strategies. Here, we show that an activating mutant of phosphoinositide-3-kinase {delta} (PI3K{delta}) led to a reduction of FoxO1-dependent TCF-1+ stem-like progenitor CD8+ T cells that are required for sustaining antigen-specific T cells in response to chronic viral infection. Nonetheless, mice expressing activated PI3K{delta} maintained CD8+ T cell responses that were skewed instead towards effector-like cells in a FoxO1-independent manner, associated with an amplified IL-21-STAT3 response axis and improved viral control. Activated PI3K{delta} limited TOX expression, prevented epigenetic changes associated with T cell exhaustion, and promoted effector differentiation and function from both progenitor stem-like cells and cells with an exhausted phenotype. Together, this work uncovers a key role for PI3K{delta} activation in shaping the balance and plasticity between effector function and exhaustion while promoting T cell persistence during chronic infection, providing insight for immunotherapeutic strategies.

immunology↗

bioRxiv2025

Engineering immunotoxin-equipped effector cells and evaluation in primary human immune cells

Lethal toxins could become potent therapies against cancer, but their clinical utility is limited by adverse events upon systemic administration. These could be reduced if the toxins were delivered by effector cells that specifically infiltrate cancers, thereby releasing toxins locally into the tumor microenvironment. One of the challenges underlying this strategy is that cells delivering toxins would have to be resistant to them. We address this obstacle by showing that effectors derived from transformed human cell lines genetically engineered for resistance to bacterial adenosine diphosphate ribosylating toxins (ADPRTs), including Pseudomonas aeruginosa exotoxin A (PE), can produce targeted immunotoxins that specifically kill cancer cells expressing cognate tumor-associated antigens. Resistance to immunotoxins was achieved by knockout of genes in the diphthamide biosynthesis pathway (DPH1-4) required for the posttranslational modification of eukaryotic elongation factor 2 (EEF2) that is the target of ADPRTs, or by mutation of EEF2 itself. We show that engineering resistance to ADPRTs, one of the most potent toxins acting on human cells, is essential to achieve robust function of armored effector cell lines. This work establishes a first step on the path to equip effector cells with the ability to deliver powerful toxins to cancer cells and introduces a platform to investigate extension to primary autologous or allogeneic therapeutic cell types.

molecular biology↗

bioRxiv2025

The HosA histone deacetylase regulates stress resistance, host cell interactions, and virulence in Aspergillus fumigatus

The capacity of Aspergillus fumigatus to cause invasive pulmonary aspergillosis depends on its ability to adapt to dynamic and stressful microenvironments within the host. Epigenetic regulation, including histone deacetylation, plays a critical role in fungal adaptation to stress. Here, we investigated the role of the class I histone deacetylase (HDAC) HosA in A. fumigatus stress resistance, host cell interactions, and virulence. A {Delta}hosA mutant had increased susceptibility to intracellular oxidant stress induced by menadione. It also had impaired capacity to invade and damage two pulmonary epithelial cell lines in vitro. In a corticosteroid-immunosuppressed mouse model of invasive aspergillosis, mice infected with the {Delta}hosA mutant survived significantly longer than those infected with the wild-type strain, despite having similar pulmonary fungal burden. The {Delta}hosA mutant also induced a weaker inflammatory response than the wild-type strain. Transcriptomic analysis revealed that HosA regulates genes involved in secondary metabolite biosynthesis and energy metabolism, functioning as both an activator and repressor of distinct gene sets. Collectively, these results indicate that HosA is a key epigenetic regulator that governs A. fumigatus interactions with host cells and virulence during invasive pulmonary aspergillosis. ImportanceEpigenetic modifications in A. fumigatus can be induced by environmental changes and stresses such as those induced by interaction with host cells. HosA, a class I histone deacetylase, has been shown to play a key role in regulating secondary metabolism in several Aspergillus species, but its function in A. fumigatus was previously unknown. We found that deletion of hosA increased susceptibility to intracellular, but not extracellular, oxidative stress. The {Delta}hosA mutant also exhibited significantly reduced pulmonary epithelial cell invasion and host cell damage, as well as attenuated virulence in immunosuppressed mice. Together, these findings indicate that HosA functions as a key epigenetic regulator that governs stress resistance, secondary metabolism, and fungal-host interactions. Defining the functions of HosA could provide critical insight into the epigenetic mechanisms that control fungal pathogenicity and may reveal a potential therapeutic target for invasive aspergillosis.

microbiology↗

bioRxiv2025

Unraveling Genomic Signatures of lncRNA Expression in Zebrafish Caudal Fin Regeneration: Bridging Regenerative Potential and Positional Memory.

Zebrafish (Danio rerio) is an essential model organism for tissue regeneration, but the function of long non-coding RNAs (lncRNAs) in tissue regeneration is not well understood. Identifying important regeneration-associated lncRNAs may allow for cross-species applications, improving tissue repair in other organisms. However, few studies and a lack of functional validation complicate our understanding of their mechanistic functions. This research explores novel lncRNAs associated with caudal fin regeneration and positional memory, aiming to identify those that are evolutionarily important across species and may hold universal significance. RNA-seq data deposited in the NCBI database were compared at various important time points (0h post-amputation (hpa), 12 hpa, 1 day post-amputation (dpa), two dpa, three dpa, and seven dpa) and fin parts (proximal, middle, and distal) to uncover major regulatory lncRNAs. Using HISAT2, StringTie, FEELnc, Conservation Analysis and WGCNA (Weighted Gene Co-expression Network Analysis), we found 107 lncRNAs related to regeneration time points and 229 about positional memory during regeneration. Overlapping analysis identified 13 common genomic regions that are complete or partial lncRNAs, indicating a functional connection between regeneration and positional identity and expressed differently in each time point and each position. Additionally, a comparison with regeneration-associated mRNAs revealed that these 13 regions play critical roles in both processes, providing insights into the molecular mechanisms of regenerative precision. Following validation by RT-PCR, the results further suggest that these overlapping regions are differentially expressed across distinct positions within the same tissue, despite a consistent injury pattern. This positional variation in expression may indicate potential roles in both evolutionary adaptation and the regulation of regenerative processes across multiple tissues.

genomics↗

bioRxiv2025

Reconstitution of multistep recruitment of ULK1 to membranes in autophagy

The Human ULK1 autophagy-initiating complex consists of ULK1, FIP200, and the HORMA domain heterodimer ATG13:ATG101. PI3P is essential to recruit ULK1C to membranes for ULK1, but ULK1C subunits do not contain PI3P-binding domains. Here we show that the ATG13:ATG101 dimer forms a complex with the PI3P-binding protein WIPI3, as well as WIPI2. Bound to WIPI2-3, ATG13:ATG101 inserts its Trp-Phe (WF) finger into the membrane. MD simulations show that WIPIs and the WF finger cooperatively stabilizes the complex on membranes. Biochemical reconstitution and cell-based assays show that WIPI3:ATG13 engagement promotes ATG16L1 phosphorylation, autophagy and mitophagy. A kinase domain (KD)-proximal PVP motif in the ULK1 IDR docks onto the ATG13:ATG101 HORMA dimer brings the ULK1 KD close to the membrane. The PVP motif is essential for in vitro ULK1 phosphorylation of ATG16L1 and important for autophagy and mitophagy. These data establish a stepwise pathway for recruitment of the ULK1 KD to the vicinity of the membrane surface.

cell biology↗

bioRxiv2025

Acute activation of Gq-signaling in islet macrophages inhibits β-cell insulin secretion through AMPK-sphingolipid axis

Obesity-associated inflammation disrupts pancreatic {beta}-cell function, but the immune-derived signals that directly regulate insulin secretion remain incompletely defined. Here, we identify myeloid Gq signaling as a critical immunometabolic node that links macrophage activation to {beta}-cell dysfunction. For the first time, we employed a chemogenetic approach (DREADDs) to selectively and temporally activate Gq-coupled GPCR signaling in myeloid cells to examine its effect on islet function. Our findings reveal that acute Gq activation in islet-resident macrophages impaired glucose-stimulated insulin secretion, uncovering a previously unrecognized immune-endocrine axis. Conversely, myeloid-specific Gq deletion improves systemic glucose homeostasis, underscoring the physiological relevance of this pathway. Mechanistic analysis revealed that Gq activation in macrophages stimulates AMPK signaling and drives the secretion of sphingolipids. These lipids suppress insulin secretion and introduce a new mechanism for immune-islet communication, extending beyond traditional cytokine-based models. We further identify the lipid-sensing receptor GPR18 as an upstream activator of the Gq-AMPK pathway in macrophages. GPR18 stimulation recapitulated the Gq-dependent sphingolipid secretion and {beta}-cell inhibitory phenotype, which was abolished in myeloid Gq-deficient mice. Collectively, these findings establish a mechanistic framework whereby macrophage Gq signaling integrates lipid sensing and metabolic stress to modulate {beta}-cell function. This work reveals a previously unrecognized macrophage-{beta}-cell communication axis with therapeutic potential for restoring insulin secretion in metabolic diseases such as obesity and type 2 diabetes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/680858v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@790c4dorg.highwire.dtl.DTLVardef@116cceborg.highwire.dtl.DTLVardef@1e76631org.highwire.dtl.DTLVardef@e65770_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells

Chimeric antigen receptor (CAR)-T cell therapies can induce drug-free remission in systemic lupus erythematosus (SLE), but indiscriminate B cell targeting causes immunosuppression, unnecessary infections, and cytokine toxicities that preclude widespread use. Here, we overcome this by targeting the 9G4 idiotope, a shared structural feature of pathogenic B cell receptors encoded by the IGHV4-34 gene. We engineered anti-9G4 CAR-T cells and chimeric TCR-T cells to selectively eliminate autoreactive B cells while preserving protective immunity. Both platforms eradicated autoreactive B cells and autoantibodies in vitro and in vivo, spared normal B cells, and markedly reduced cytokine release compared to conventional CAR-T cells. This precision extended to cold agglutinin disease and lymphoma. These findings establish a framework for IGHV idiotope-directed cellular therapies for treating autoimmune and neoplastic diseases while preserving immune competence.

immunology↗

bioRxiv2025

Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells

Transcriptional regulation of transposons and genes by TRIM28 and 5mC is critical for proper mammalian embryonic development, but the specific roles for these mediators in human embryonic and placental lineage remain unclear. We find that loss of TRIM28 has a limited effect on global transposon expression and instead results in upregulation of genes proximal to TRIM28-bound Long Terminal Repeats (LTRs) in both human trophoblast stem cells (hTSCs) and human embryonic stem cells (hESCs). MER11A elements show especially strong regulatory importance in hTSCs: these elements are bound by both TRIM28 and placental transcription factors and show both heterochromatic and euchromatic features. Some genes are positively regulated by MER11A elements in hTSC basal state, while other MER11A-proximal genes show upregulation only upon TRIM28 deletion. By contrast, loss of DNA methylation in hESCs or hTSCs leads to a global increase in transposon expression. While many genic 5mC targets are shared in hESCs and hTSCs, we also observe evidence that a handful of genes important for somatic development are repressed by 5mC in trophoblast, while a small parallel set of placental genes are repressed by methylation in embryonic tissue. Interestingly, loss of DNMT1 causes hESCs to be rapidly lost from culture in a TP53 and mitotic surveillance checkpoint-dependent manner, while hTSCs show little p53 response to DNMT1 loss or DNA damage generally, instead showing gradual mitotic defects and aneuploidy and slow loss from culture. This discrepancy may explain the higher frequency of karyotypic abnormality found in human placental cells. Together, this study charts the role of TRIM28 and DNA methylation in regulating embryonic and placental transcription and demonstrates divergent p53-dependent responses to genomic instability.

molecular biology↗

bioRxiv2025

Candida albicans activates Staphylococcus aureus virulence regulatory systems to drive toxin-mediated human cell death

Co-infection with Staphylococcus aureus and Candida albicans leads to worsened disease severity compared to mono-microbial infection. Because our understanding of the mechanisms driving enhanced disease severity during co-infection is limited, we sought to evaluate how interactions with C. albicans regulate S. aureus virulence towards host cells. We determined that C. albicans enhances S. aureus cytotoxicity towards murine monocytes via a mechanism requiring the Agr system. Agr is a major regulator of S. aureus virulence factors and was previously shown to be activated by C. albicans, but the Agr-regulated virulence factors driving immune cell death are unknown. We identified that enhanced murine monocyte cell death requires the -type phenol soluble modulins and {psi}-hemolysin. Because several S. aureus toxins have species-specific effects, we also tested how co-culture impacts cytotoxicity towards human monocytes. Unexpectedly, we discovered that C. albicans induces robust cytotoxicity of an S. aureus agr mutant ({Delta}agr), which is completely non-toxic towards murine monocytes. Using reporter strains and combinatorial mutants, we identified that co-culture activates the SaeRS regulatory system in S. aureus, and SaeRS is required for human-specific cytotoxicity. We further discovered that the SaeRS-regulated toxin Panton-Valentine Leukocidin (PVL) drives S. aureus {Delta}agr cytotoxicity following co-culture. Finally, we observed similar cytotoxicity phenotypes using both S. aureus and C. albicans clinical isolates, demonstrating broad conservation of this interaction. Interestingly, the magnitude by which C. albicans isolates induce cytotoxicity of S. aureus {Delta}agr varies among strains tested. Overall, this study identifies that C. albicans activates a major S. aureus virulence regulatory system in a typically non-toxic strain, triggering S. aureus to induce potent human-selective cell death.

microbiology↗

bioRxiv2025

Arginine methyltransferase PRMT1 equipoises trophoblast development to prevent early pregnancy loss

Abstract1-2% of all human pregnancies suffer from idiopathic recurrent pregnancy loss (RPL) and underlying molecular causes are poorly understood. Here we show that defective Protein Arginine Methyltransferase 1 (PRMT1) function in trophoblast progenitors is a molecular cause for early pregnancy failure. PRMT1 is conserved in trophoblast progenitors and conditional deletion of PRMT1 in mouse trophoblast progenitors arrests placenta and embryonic development leading to lethality [~]E7.5. Remarkably, a subset of idiopathic RPL is associated with loss of PRMT1 in cytotrophoblast progenitors (CTBs). Experiments with human trophoblast stem cells (hTSCs), derived from these RPL-patients as well as PRMT1-depleted hTSCs revealed that PRMT1 is crucial for trophoblast progenitors self-renewal. Employing RNA-seq and CUT&RUN-sequencing in hTSCs, CTBs and primary mouse trophoblast progenitors we discover that PRMT1 promotes transcription of trophoblast stem-state regulators, like TEAD4 and MYBL2, by directly enriching histone H4 arginine 3 asymmetric di-methylation (H4R3Me2a) at their chromatin loci. PRMT1 is also essential for extravillous trophoblast (EVT) development during human placentation, while loss of PRMT1 in hTSCs spontaneously promotes syncytiotrophoblast (STB) differentiation. Our findings indicate that PRMT1 is an epigenetic governor that orchestrates mammalian trophoblast development and implicate the therapeutic potential of targeting the PRMT1-H4R3Me2a axis to mitigate early pregnancy loss.

developmental biology↗

bioRxiv2025

Automated Eight-Stage Classification of Drosophila melanogaster Using Transfer-Learning CNNs with Mobile Live-Inference Deployment

Drosophila melanogaster is a foundational model organism whose rapid development and genetic tractability underpin research in genetics, development, and disease. Manual staging of its embryonic, larval, and pupal phases is slow and error-prone. An automated eight-class classifier is introduced to distinguish egg, first-, second-, and third-instar larvae, as well as white, brown, eye, and black pupae, from stereo-microscope images. By fine-tuning ImageNet-pretrained CNNs (ResNet-50, InceptionV3, ConvNeXtSmall) on a balanced dataset ([~]300 images per class), the best-performing model (ResNet-50) achieves 85% accuracy (F1 = 0.85) on a held-out validation set, significantly outperformed alternatives. Primary misclassifications align with subtle morphological transitions between adjacent stages. To facilitate broad adoption, the ResNet-50 model has been deployed in a lightweight Streamlit app offering live-camera inference ({approx}8 FPS on mobile). All code, pretrained weights, and data are publicly available, enabling scalable, high-throughput Drosophila staging for diverse experimental workflows.

bioinformatics↗

bioRxiv2025

Exploring the evolutionary divergence of cyclic di-nucleotide signaling in diverse mycobacterial species

Cyclic dinucleotides (CDNs), such as cyclic di-AMP (c-di-AMP) and cyclic di-GMP (c-di-GMP), are key second messengers that regulate fundamental bacterial processes, including cell wall synthesis, biofilm formation, antibiotic resistance, stress response, and virulence. These pathways are particularly relevant in major pathogens like Mycobacterium tuberculosis. Increasing evidence highlights the pathogenic potential of non-tuberculous mycobacteria (NTM), originally environmental species that are emerging as significant human pathogens. Understanding the evolution of CDN signaling may therefore provide critical insights into this transition. Our comparative genomic analysis revealed that the c-di-AMP synthase disA is present as a single copy in nearly all mycobacterial genomes, except within the genus Mycolicibacter. The corresponding phosphodiesterases, PDE and AtaC, are variably distributed, with pathogenic mycobacteria showing a preference for PDE over AtaC. In contrast to the relatively conserved c-di-AMP system, the c-di-GMP pathway comprising diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), exhibits remarkable variation in gene presence/absence and domain architecture across the Mycobacteriaceae family. This diversity suggests multiple independent gene gain and loss events throughout evolution, often accompanied by the acquisition of accessory domains. Evolutionary analyses indicate that disA, like core housekeeping genes, is under strong purifying selection, while pde shows relatively low diversity, reinforcing the idea that c-di-AMP signaling is highly conserved and essential across mycobacteria. By contrast, the c-di-GMP system is more heterogeneous, reflecting its role in environmental adaptation. Together, these findings highlight a sharp evolutionary divergence in CDN signaling, where c-di-AMP appears indispensable for core physiology, whereas c-di-GMP provides flexibility for niche-specific adaptation within the Mycobacterium genus.

microbiology↗

bioRxiv2025

Lepr Haploinsufficiency Accelerates Alzheimer-like Neurodegeneration via CDK5 Hyperactivation

Leptin signaling has neuroprotective effects and is increasingly linked to Alzheimers disease (AD). Beyond metabolism, leptin modulates {beta}-amyloid metabolism, tau phosphorylation, and synaptic plasticity. While homozygous Lepr mutations are well studied, the impact of heterozygous mutations on neurodegeneration is unclear. To assess partial Lepr loss, one-year-old db/+ mice were evaluated for metabolic, behavioral, and neuropathological changes. Tests included glucose tolerance, memory assays, A{beta}42 and tau levels, CDK5 activity, and transcriptomics. Human LEPR variants were curated and classified using ACMG guidelines. Aged db/+ mice showed metabolic dysfunction, cognitive deficits, and AD-like pathology. Compared to controls, db/+ mice had increased body weight, insulin resistance, memory impairments, elevated A{beta}42, tau hyperphosphorylation, CDK5 hyperactivation, and astrocyte activation. Transcriptomics revealed altered synaptic and mitochondrial pathways. Thirty-three pathogenic or likely pathogenic human LEPR variants were identified. Lepr haploinsufficiency contributes to age-related cognitive decline and AD-like pathology, suggesting it as a genetic risk factor and therapeutic target.

neuroscience↗

bioRxiv2025

A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML

Patients with myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) with high-risk features including TP53 mutations and deletions have poor outcomes due to lack of effective therapies. The atypical chemokine surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in MDS and secondary AML (sAML) compared to healthy hematopoietic cells and we recently found that TP53-mutated MDS/AML and AML with erythroid features express the highest levels of this receptor across MDS/AML subtypes. To illustrate the therapeutic potential of CCRL2 as a therapeutic target, we developed an anti-CCRL2 antibody-drug conjugate (ADC) by conjugating an anti-CCRL2 antibody with the cytotoxic drug pyrrolobenzodiazepine (PBD), which causes DNA double-strand breaks leading to cancer cell death. The anti-CCRL2 ADC demonstrated strong CCRL2-selective cytotoxicity against cell lines derived from MDS/AML patients with TP53 mutations and erythroid features, surpassing the cytotoxic effects observed with gemtuzumab and PBD-conjugated anti-CD33 and anti-CD123 ADCs. It also induced apoptosis and suppressed the clonogenicity of primary MDS/AML bone marrow samples without affecting the survival, differentiation and clonogenicity of healthy hematopoietic stem and progenitor cells. This agent also suppressed the leukemic growth of TP53-mutated MDS/AML cell line xenografts, improving mice survival and decreasing the leukemic burden in patient-derived TP53-mutated MDS/AML xenografts. In conclusion, our study introduces CCRL2 as a potential new therapeutic target in high-risk MDS/AML. Statement of significancePyrrolobenzodiazepine(PBD)-conjugated anti-CCRL2 ADC shows anti-leukemic effect in MDS/AML models including TP53-mutated disease without affecting healthy hematopoietic cells supporting that it is a promising candidate for single-agent or combination therapies in high-risk MDS/AML.

cancer biology↗

bioRxiv2025

Topoisomerase II inhibitors CX-5461 and Doxorubicin differ in their cardiotoxicity profiles

CX-5461 (CX) is a chemotherapeutic drug currently under investigation for the treatment of late-stage cancers. While CX was first described as an RNA polymerase I inhibitor, it has recently been shown to primarily inhibit the beta isoform of topoisomerase II. This isoform is also inhibited by anthracycline drugs including Doxorubicin (DOX) and mediates the toxic effects of these drugs on the heart. It is unclear whether CX will similarly cause cardiotoxicity. We therefore designed a study to test the effects of CX compared to DOX on iPSC-derived cardiomyocytes from six individuals. While both CX and DOX induce cell death in cardiomyocytes, CX is 20-fold less cytotoxic than DOX. At sub-lethal doses, DOX induces DNA damage, while CX does not. Transcriptome profiling following treatment with two sub-micromolar concentrations of both drugs over time reveals that DOX induces thousands of gene expression changes compared to hundreds induced by CX. Comparison of gene expression trajectories across drugs reveals that genes that respond to CX also respond to DOX, while most DOX response genes are drug specific. Shared response genes correspond to pathways related to chromosome segregation and DNA replication. CX does not affect the expression of any of the genes in functionally-validated loci associated with DOX-induced cardiotoxicity. Our data demonstrate that CX treatment of cardiomyocytes induces gene expression changes that mirror a subset of those induced by DOX; however these changes do not coincide with the cardiotoxicity observed with DOX treatment.

genomics↗