Biology subjects

Biswas, P.

Publications and source records attributed to Biswas, P..

At least 19 recordsLinked to original sources

bioRxiv2026

CBFA2T3-GLIS2 establishes transcriptionally permissive enhancer hypermethylation associated with venetoclax response in pediatric AML

CBFA2T3-GLIS2 (C/G) defines a high-risk pediatric AML subtype in which de novo enhancer rewiring sustains an aggressive leukemic transcriptional state. The early epigenomic mechanisms reinforcing this program and linking it to leukemic survival remain incompletely defined. Here, we identify enhancer-proximal hypermethylation as a noncanonical, transcription-permissive feature of C/G AML. Using primary C/G-positive AML samples and a developmentally relevant C/G-transformed cord blood hematopoietic stem/progenitor cell model, we integrated DNA methylation, chromatin state, fusion occupancy, and gene expression across early and leukemia-stage contexts. Early C/G-associated hypermethylated regions localized near H3K27ac/H3K4me1-marked active or primed cis-regulatory elements, were enriched for ERG/ETS-like motifs, and showed related architecture in leukemia-stage contexts. DNMT3B was prominently increased in C/G contexts, and its loss selectively altered methylation-associated gene expression without measurably changing global 5mC. Genetic DNMT3B loss increased venetoclax sensitivity in vitro, while pharmacologic DNMT3B inhibition with Nanaomycin-A similarly enhanced venetoclax response. During venetoclax treatment, DNMT3B-deficient xenografts showed reduced disease burden and prolonged survival. To assess whether this interaction extended to clinically used hypomethylating agents, azacitidine or decitabine plus venetoclax induced apoptosis-related transcriptional programs and mitochondrial depolarization. These findings identify hypermethylated active cis-regulatory elements as C/G-associated states linked to transcriptional dysregulation and venetoclax response.

cancer biology↗

bioRxiv2026

Soluble guanylyl cyclase subunits act as Hsp90 co-chaperones to ensure the expression and functional maturation of hemeproteins in mammalian cells

The cofactor Fe-protoporphyrin IX cofactor (heme) performs many functions in biology. Animal cells must stabilize their newly generated heme-free (apo)-hemeproteins and deliver mitochondrial heme to them so they can mature to functional form. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) typically accomplishes the heme deliveries, and for many apo-hemeproteins, heat shock protein 90 (Hsp90) drives their heme insertions. We previously observed hemeproteins express poorly in a cell line (COS-7) that does not express soluble guanylyl cyclase (sGC), a heme-binding enzyme that typically functions through its cGMP generation. To understand sGC involvement, we expressed four hemeproteins, Hemoglobin beta (Hb{beta}), Myoglobin (Mb), Indoleamine 2,3-dioxygenase 1 (IDO1), and Tryptophan 2,3-dioxygenase (TDO) in a cell line expressing sGC (HEK293) or in two cell lines (COS-7, DU145) that do not. We assessed hemeprotein expression levels, their abilities to acquire heme, and when relevant if these facets could be rescued by co-expressing individual sGC subunits, including variants with defects in either sGC heme binding, Hsp90 association, heterodimerization, or cGMP production. We found that co-expression of either sGC subunit was essential for three of the four apo-hemeproteins to accumulate in the COS7 and DU145 cells and acquire heme. This did not involve heme binding, heterodimer formation, or cGMP generation by the sGC subunits, and instead depended on a subunits ability to recruit Hsp90 and GAPDH to the apo-hemeproteins via their own Hsp90 binding. Recruiting Hsp90 and GAPDH to apo-hemeprotein clients to ensure they can accumulate and mature to functional form broadens our understanding of sGC and Hsp90 functions in biology.

cell biology↗

bioRxiv2026

DAAM1 formin and Ena/VASP proteins assemble functionally distinct actin filaments for focal adhesions

Eukaryotic cells contain multiple biochemically distinct actin filament networks, which enable versatile functions of actin in a range of cellular processes. Yet, the mechanisms by which specific actin filament networks are assembled in a common cytoplasm remain elusive. Here, we investigated how functionally distinct actin nanoscale layers, specified by -actininand tropomyosin isoforms, Tpm1.6 and Tpm3.2, are assembled at focal adhesions. By combining genetic perturbations with mitochondrial-targeting of actin polymerases, we discovered that DAAM1 formin assembles Tpm3.2-actin filaments, whereas Ena/VASP family proteins polymerize -actinin cross-linked actin filament bundles at focal adhesions. Consequently, loss of DAAM1 dampened Tpm3.2 protein levels and impaired focal adhesion disassembly, thus phenocopying Tpm3.2-deficient cells. In contrast, Ena/VASP depletion led to defective focal adhesion maturation and loss of -actinin from focal adhesions. More broadly, our study highlights specific roles for formin and Ena/VASP family proteins in assembling biochemically and functionally distinct linear actin filament arrays in cells.

cell biology↗

bioRxiv2026

Citrobacter rodentium infection reveals preserved intestinal resilience in aged intestine

Ageing is generally associated with increased susceptibility to enteric infection and is widely considered to reflect progressive deterioration of intestinal function. However, whether increased susceptibility represents complete loss of intestinal resilience or a distinct host response to infection remains unclear. Using Citrobacter rodentium (CR) infection as a model of infectious colitis, we investigated how ageing shapes epithelial responses to enteric bacterial infection. Infection of aged mice with wild type CR (CRWT) resulted greater bacterial colonisation, deeper crypt localisation, impaired fluid-ion homeostasis and more severe colitis than young mice. Conversely, infection of aged mice with CRM12, a CR strain lacking 12 type III secretion system effectors, resulted in reduced epithelial colonisation, preservation of epithelial barrier function and fluid-ion homeostasis, restrained inflammatory responses, and markedly lower disease severity than CRWT infection. Deep quantitative proteomic analysis demonstrated that these divergent outcomes were accompanied by distinct adaptive molecular programmes within the aged intestinal epithelium. Together, our findings demonstrate that although aged mice exhibit increased susceptibility to enteric infection, the aged intestine retains the ability to mount distinct epithelial, inflammatory and molecular responses to pathogens with different virulence repertoires. Thus, increased susceptibility in aged mice should not be interpreted as complete loss of intestinal resilience.

microbiology↗

bioRxiv2026

HF-125, a first-in-class computer-modeled novel inhibitor of Tribbles 2, for therapy of enzalutamide resistant, neuroendocrine prostate cancer.

Second generation antiandrogens, such as enzalutamide, are commonly prescribed to treat advanced prostate cancer. However, enzalutamide resistant prostate cancer (ERPC) invariably develops with more aggressive features. Management of ERPC is extremely difficult not only because available therapies cannot effectively eliminate ERPC cells but also due to enhanced growth and highly metastatic features in ERPC cells to invade distant organs. This problem is amplified by the lack of proper knowledge about suitable molecular targets in ERPC cells. Recently, we reported that Tribbles 2 (TRIB2), is overexpressed in ERPC cells and tumors and inhibition of TRIB2 kills ERPC cells via apoptosis. TRIB2 enhances cancer cell growth and invasion and confers resistance to enzalutamide, while inhibition of TRIB2 resensitizes the resistant cells. Interestingly, TRIB2 induces neuroendocrine (NE) features in ERPC cells and both the de novo and treatment-emergent NEPC cells consistently overexpress TRIB2. Though TRIB2 has emerged as a promising target, suitable inhibitors are not commercially available for clinical use. We used artificial intelligence (AI)-based molecular modeling to design a series of small chemical entities with potentially high specificity to bind with TRIB2. Extensive virtual screening and molecular editing yielded few highly selective and potent agents to inhibit TRIB2 and kill ERPC-NE/NEPC cells. One such compound (HF-125) directly binds to destabilize and degrade TRIB2 proteins involving proteasomes and is effective both in vitro and in vivo. Based on these findings, HF-125 emerges as a promising novel agent for development of a new therapeutic strategy for ERPC-NE/NEPC types of aggressive prostate cancer.

cancer biology↗

bioRxiv2026

In Vitro Prebiotic Potential of Purified Black Rice Oligosaccharides: Simulated Digestion Stability, Short-Chain Fatty Acid Production, and Probiotic Biofilm Formation

Black rice oligosaccharides (BO) were extracted with 80% aqueous ethanol (v/v) and purified by charcoal-celite chromatography followed by dialysis using a 500 Da molecular weight cut-off (MWCO) membrane, yielding an oligosaccharide fraction with a degree of polymerisation (DP) between three and eight (DP3-DP8; 2.87 {+/-} 0.29% w/w). MALDI-TOF MS showed sodium adduct ions from m/z 527 to 1330, and GC-MS analysis of hydrolysed samples identified glucose and galactose as the major monomers, while ketosyl residues were detected in the intact fraction by selective staining and are most plausibly attributed to fructosyl units based on cereal origin and DP distribution. BO showed high resistance to simulated salivary, gastric, and pancreatic digestion (only 2.08 {+/-} 0.51%, 0.34 {+/-} 0.03%, and 4.29 {+/-} 0.73% hydrolysis, respectively) with approximately 93% remaining carbohydrate available for fermentation. All Lactobacillus strains showed positive prebiotic activity scores, with the highest response observed for Lactobacillus rhamnosus (1.165 {+/-} 0.255) and Lactobacillus plantarum (0.980 {+/-} 0.163). Fermentation produced metabolically relevant short-chain fatty acids (SCFA), mainly acetate (34.82 {+/-} 2.08 mM), as well as strain-dependent propionate and butyrate levels. BO greatly promoted probiotic biofilm formation, with biomass reaching 391.33 {+/-} 26.08% and viable cell counts of 9.01 {+/-} 0.70 log CFU/mL relative to the control. Collectively, the results indicate that BO represents a digestion-resistant, hexose-based oligosaccharide series that is selectively utilised by probiotic lactobacilli, promotes SCFA production and enhances biofilm development. To our knowledge, this work is the first to combine structural profiling with in vitro functional evaluation of a purified, low-DP oligosaccharide fraction obtained from black rice. HighlightsO_LIPurified oligosaccharides (DP3-DP8) were obtained from black rice using charcoal-celite chromatography followed by dialysis. C_LIO_LIStructural analysis confirmed that the oligosaccharides were hexose-based and composed mainly of glucose and galactose. C_LIO_LIBlack rice oligosaccharides exhibited higher resistance to simulated gastric and intestinal digestion compared with starch. C_LIO_LIPositive prebiotic activity scores were observed due to selective utilisation by probiotic Lactobacillus strains. C_LIO_LIFermentation of black rice oligosaccharides significantly increased short-chain fatty acid production. C_LIO_LIPurified oligosaccharides enhanced probiotic biofilm formation, indicating improved colonisation potential. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/705216v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@9a5915org.highwire.dtl.DTLVardef@14eac7aorg.highwire.dtl.DTLVardef@1db8baorg.highwire.dtl.DTLVardef@14ad50a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Recombinant Lactococcus lactis-based multivalent vaccine targeting Campylobacter jejuni colonisation and modulating cecal microbiota in poultry

BackgroundDiarrhoeal diseases remain the second leading cause of preventable death globally, particularly among children under the age of five in developing countries, accounting for an estimated 2-3 million deaths annually. Among the bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains one of the major contributors, particularly in LMICs. As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonisation proteins, namely Hcp, VgrG, CadF, FlpA, and JlpA. Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion in avian and non-avian hosts. MethodsTo minimise the C. jejuni adhesion and subsequent colonisation in the avian gut, we explored the potential of a multivalent mucosal vaccine composition using these putative subunits of C. jejuni. For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits, Hcp, CadF and JlpA. Utilising this live vector-based multi-component mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonising, we used chitosan as a natural mucoadhesive, biodegradable polymer to microencapsulate the engineered bacteria to increase their gut retention time for optimal interaction with local immune cells. ResultsOur in vivo immunisation study demonstrated that oral administration of this multivalent vaccine formulation elicited a strong local antibody response (sIgA) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection against the cecal colonisation of C. jejuni. Moreover, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota, accompanied by an increased abundance of the phyla Bacillota and Bacteroidota, as part of a beneficial microbial community. ConclusionsTogether, this study underscores the potential of a live vector-based, multivalent mucosal vaccine as a promising, cost-effective strategy to reduce the risk of foodborne transmission of C. jejuni, particularly in poultry production systems.

immunology↗

bioRxiv2025

GBP1 recruitment to actin-rich pedestals induced by extracellular Gram-negative bacteria promotes pyroptosis.

The IFN{gamma}-induced GTPase guanylate binding protein 1 (GBP1) binds to lipopolysaccharide (LPS) on cytosolic Gram-negative bacteria and promotes pyroptosis via the recruitment and activation of caspase-4 on the bacterial outer membrane. Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC, respectively) are extracellular pathogens that also induce LPS-and caspase-4-dependent pyroptosis. However, whether GBP1 is involved in this process remains unknown. EPEC and EHEC adhere intimately to intestinal epithelial cells via avid interactions between the bacterial adhesin Intimin and Tir (Translocated intimin receptor), a type 3 secretion system effector protein. Intimin-mediated clustering of Tir triggers actin polymerisation, leading to pedestal-like structures at bacterial attachment sites. Here we show that GBP1 is recruited to actin-rich pedestals in human cells infected with EPEC and EHEC in vitro and mouse colonocytes infected with the EPEC-like murine pathogen Citrobacter rodentium in vivo. GBP1-dependent caspase-4 trafficking to these sites leads to pyroptosis and IL-18 release. GBP1 mutants defective in LPS coatomer formation also localised to EPEC pedestals, pointing to LPS-independent mobilisation of GBP1 by actin polymerisation induced by extracellular A/E pathogens. To further dissect the underlying mechanism, we engineered a chimeric receptor (Fc{gamma}R-Tir) by combining the intracellular signalling domain of Tir and the extracellular ligand-binding domain of the Fc{gamma} receptor. Clustering of Fc{gamma}R-Tir with IgG-coated beads produced sterile actin-rich pedestals that were sufficient to recruit GBP1 independently of bacteria. Our findings reveal that cytosolic GBP1 is mobilised to sites of pathogen-induced actin remodelling independently of LPS. We establish that GBP1 not only operates as a pattern-recognition receptor but also orchestrates effector-triggered immunity against pathogens that hijack the actin cytoskeleton. 175-word AbstractThe IFN{gamma}-induced GTPase guanylate binding protein 1 (GBP1) binds to lipopolysaccharide (LPS) on cytosolic Gram-negative bacteria and promotes pyroptosis via the recruitment and activation of caspase-4 on the bacterial outer membrane. Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC, respectively) are extracellular pathogens that adhere to host cells and stimulate dense actin polymerisation underneath their attachment sites, generating structures called actin-rich pedestals. Here we show that GBP1 traffics to actin-rich pedestals in human cells infected with EPEC and EHEC in vitro and mouse colonocytes infected with the EPEC-like murine pathogen Citrobacter rodentium in vivo. GBP1 promotes caspase-4 recruitment to actin-rich pedestals, leading to pyroptosis and IL-18 release. GBP1 mutants defective in LPS coatomer formation also localised to EPEC pedestals. Our novel assay that mimics pathogenic effector activity revealed GBP1 recruitment to sterile actin polymerisation sites. We conclude that cytosolic GBP1 is mobilised to sites of pathogen-induced actin remodelling independently of LPS. Our study establishes that GBP1 not only operates as a pattern-recognition receptor but also orchestrates effector-triggered immunity against pathogens that hijack the actin cytoskeleton.

immunology↗

bioRxiv2025

Sex-biased expression of enteroendocrine cell-derived hormones contributes to higher fat storage in Drosophila females

Enteroendocrine (EE) cells in the Drosophila gut produce and release multiple factors, including Allatostatin A (AstA), Allatostatin C (AstC), neuropeptide F (NPF), tachykinin (Tk), Diuretic hormone 31 (Dh31), Bursicon, CCHamide 1, CCHamide 2, and short neuropeptide-F. Collectively, these peptides ensure that physiology (e.g., fat storage, fluid balance) and behavior (e.g., feeding, sleep) are coordinated with environmental factors such as nutrient quantity and quality. Despite notable sex differences in physiology and behavior, it remains unclear whether the regulation and function of these EE cell-derived factors are shared between males and females. Given that recent data identified sex-biased physiological effects of two EE cell-derived hormones on Drosophila food intake and energy mobilization, we performed a detailed characterization of these hormones in male and female flies. Despite an overall male bias in mRNA levels of AstA, AstC, Tk, NPF, Dh31 in whole-body and head samples, we observed a strong female bias in mRNA levels of AstC, Tk, and NPF in the gut. To determine whether this sex-biased regulation was physiologically significant, we monitored triglyceride levels in flies with gut-specific knock-down of EE cell-derived hormones. In 5-day-old flies, knock-down of EE cell-derived AstC significantly reduced fat storage in females with no effect in males, whereas knock-down of EE cell-derived Tk produced a non-significant trend toward reduced fat storage in females. These female-specific effects on fat storage were reproduced in flies with neuron-specific knock-down of the AstC (AstC-R2) and Tk receptors (TkR99D). Together, these data uncover strongly sex-biased regulation of EE cell-derived hormones, and show that gut-specific knock-down of at least one of these hormones had a female-specific effect on body fat. HighlightsO_LIEnteroendocrine cell-expressed hormones show strongly sex-biased expression C_LIO_LIKnock-down of enteroendocrine cell-derived AstC reduced body fat only in females C_LIO_LINeuronal knock-down of AstC or Tk receptors reduced stored fat only in females C_LI

physiology↗

bioRxiv2025

Cell type specific allometry controls sex-differences in Drosophila body size

Species and sex-specific differences in organ size are fundamental features of animal biology, yet the mechanisms that drive these differences remain debated. Adult female Drosophila are larger than males. While most organs are present across both sexes, the underlying mechanisms driving sex-specific organ and body size scaling of Drosophila remain unclear. Using single-nucleus transcriptomes from the Fly Cell Atlas, combined with experimental validation, we show that different Drosophila organs scale through distinct strategies, including cell size, cell number, or a combination of both, in an allometric rather than uniform manner. Larger female flight muscles develop from more myoblasts than in males, while cardiomyocyte numbers are the same despite forming a larger heart in females. Female fat body cells are larger and express more ribosomal protein-coding mRNAs, supporting increased cell size. In contrast, males have a greater number of fat body cells. Together, this sex-specific allometry in cell size and number define the cellular basis for differences in body and organ size between sexes in Drosophila. By uncovering how a conserved developmental system produces sex-specific proportions through distinct cellular strategies, our work offers a framework for dissecting sex differences in other species and systems.

cell biology↗

bioRxiv2025

Multi-omic analysis of photoreceptor alterations during early-onset retinal degeneration in Mfrp-/- mice

Loss-of-function mutations in the membrane frizzled-related protein (MFRP) gene are associated with autosomal recessive ocular disorders such as nanophthalmos, posterior microphthalmia, and retinitis pigmentosa, yet the molecular mechanisms underlying MFRP-related retinal degeneration remain poorly defined. To investigate these mechanisms, we generated and characterized Mfrp-/- mice and conducted an integrated multi-omic analysis to map the onset and progression of transcriptional changes during retinal degeneration. Using longitudinal in vivo imaging, histological and immunohistochemical analysis, qRT-PCR, single-nucleus RNA sequencing (snRNA-seq), snATAC seq (single-nucleus Assay for Transposase-Accessible Chromatin using sequencing) and spatial transcriptomics (GeoMx DSP), we identified early and progressive photoreceptor loss in Mfrp-/- mice, beginning by 28d. Retinal thinning and autofluorescent deposits in Mfrp-/- mice were accompanied by decreased expression of rod and cone opsins. Transcriptomic profiling by snRNA-seq revealed distinct, photoreceptor-specific gene expression changes, including early upregulation of inflammatory and stress-related genes and later downregulation of genes involved in chromatin remodeling, synaptic function, and neurodevelopment. Spatial transcriptomic analysis of the outer nuclear layer (ONL) revealed disruptions in mitochondrial function, mTORC1 signaling, and G protein-coupled receptor pathways. These findings define a temporally and spatially coordinated program of degeneration triggered by Mfrp loss and demonstrate that Mfrp is required for the maintenance of photoreceptor integrity and gene regulatory homeostasis during retinal development. Our work establishes Mfrp-/- mice as a robust model for dissecting photoreceptor vulnerability and provides a transcriptomic atlas of disease progression with potential relevance for therapeutic development in MFRP-associated retinal dystrophies.

genomics↗

bioRxiv2025

Enteric infection priming confers IL-17A dependent protection from chemically-induced Colitis

Background and AimsEnteric infections trigger mucosal immune responses. However, whether such immune imprinting influences susceptibility to sterile inflammatory diseases like colitis remains unclear. The aims of this study were to investigate whether a resolved Citrobacter rodentium (CR) infection in mouse alters host susceptibility to chemically induced colitis and to identify the underlying immune mechanisms. MethodsC57BL/6 mice were infected with wild-type CR or CR {Delta}map{Delta}espF, a mutant lacking tight junction-disrupting effectors. 3 weeks post clearance, mice were subjected to dextran sodium sulfate (DSS)-induced colitis. Disease severity was assessed by weight change, colon length, histopathology, and myeloperoxidase levels. Colonic immune cell populations were characterised by flow cytometry, and cytokine levels were measured from colon explants. Functional roles of IL-17A were evaluated using recombinant cytokine administration and neutralising antibody treatment. ResultsMice that cleared CR infection fared better following DSS treatment compared to uninfected or {Delta}map{Delta}espF-infected mice. This protective phenotype was not directly dependent on microbiota, as confirmed by co-housing experiments. Protected mice displayed elevated numbers of colonic Th1 and Th17 cells and higher levels of IL-17A, IL-22, and IL-2 cytokines. Prophylactic treatment with IL-17A conferred protection in naive mice, whereas IL-17A neutralisation in previously infected mice abrogated the benefit, identifying IL-17A as a key mediator of protection. ConclusionsResolved intestinal infection with CR confers long-term protection against colitis via persistent IL-17A-mediated immune reprogramming. These findings resonate with the "hygiene hypothesis" and highlight how prior microbial exposure can shape mucosal resilience.

microbiology↗

bioRxiv2025

The accessory type III secretion system effectors shape intestinal inflammatory infection outcomes

Injection of effectors via a type III secretion system (T3SS) is an infection strategy shared by various Gram-negative bacterial pathogens, many infecting mucosal surfaces. While individual T3SS effectors are well characterized, their network-level organization and the distinction between core and accessory effectors remain incompletely understood. Here, by systematically dissecting the T3SS effector network of the enteric mouse pathogen Citrobacter rodentium (CR) we identified a subset of 12 accessory effectors that, while dispensable for colonization, significantly alter infection outcomes. A strain lacking the accessory effectors (CRM12) remained virulent in susceptible mouse hosts yet resulted in reduced epithelial barrier damage, inflammation, and immune cell infiltration in resistant mice. Deep proteomic analysis specifically targeting CR-attached colonic epithelial cells revealed that, despite lacking 39% of its effector repertoire, infection with CRM12 results in similar changes to global protein expression as seen in mice infected with the wild-type strain, though key regulators of barrier integrity were differentially expressed. Using a host model with impaired barrier repair, we confirmed that accessory effectors shape infection outcomes without significantly impacting virulence. This study refines the concept of core and accessory effectors, providing a basis for further studies into effector-driven host adaptation.

microbiology↗

bioRxiv2025

IL-18 activates mucosal group 2 innate lymphoid cells following enteric bacterial infection

Group 3 innate lymphoid cells (ILC3s) play a major role in protecting against infection with the enteric mouse pathogen Citrobacter rodentium, used to model infections with enteropathogenic and enterohaemorrhagic Escherichia coli. ILC3s-secreted IL-22, shown to be indispensable for protection against C. rodentium infection, induces secretion of IL-18, antimicrobial peptides and nutritional immunity proteins as well as activation of tissue regeneration processes. While ILC2s have traditionally been associated with immune responses to helminth infection and allergic inflammation via the production of type 2 cytokines (e.g. IL-4, IL-5, IL-9 and IL-13), more recently they have been implicated in protection against Clostridium difficile and Helicobacter pylori infections. Here we show that colonic lamina propria ILC2s proliferate in response to C. rodentium infection and secrete IL-4, IL-5 and IL-13, which are involved in maintenance of the intestinal barrier function, tissue repair and mucus secretion. When stimulated with IL-18, colonic ILC2s from uninfected naive mice secreted type 2 cytokines. Injection of IL-18 binding protein (IL18BP), at 2- and 3-days post C. rodentium infection, blocked activation of ILC2s. These data show that ILC2s are activated in response to infection with an enteric Gram-negative pathogen, where stimulation with IL-18 plays a role in inducing proliferation and secretion of type 2 cytokines. Author SummaryWhile group 3 innate lymphoid cells (ILC3s) play a key role in protecting from bacterial infections, ILC2s are mainly associated with immune responses to helminth infection. Here we investigated if ILC2s are activated in responses to infection with the enteric mouse pathogen Citrobacter rodentium. We show that in infected mice, gut ILC2s expand and secreted type 2 cytokines. ILC2 isolated from uninfected mice were activated by IL-18. Consistently, administration of IL-18 binding protein into C. rodentium-infected mice inhibited ILC2 activation. These findings suggest that gut ILC2s are activated by Gram negative enteric pathogens, which is mediated in part by IL-18.

immunology↗

bioRxiv2024

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

genomics↗

bioRxiv2024

Thermal Plasticity of Stage Specific Development Time in Drosophila melanogaster under Shifting Temperatures

We examined how thermal shifts influence development time and adult body size in Drosophila melanogaster. Individual flies were exposed to alternating temperatures of 25{degrees}C (optimal) and 17{degrees}C (cold), with shifts introduced at key developmental transitions: larval hatching and pupariation. We found while larval-stage temperature is the biggest determinant of thermal plasticity of development time and adult size, the egg-stage temperature also influences the pace of development and growth throughout pre-adult duration. The effect of low-to-high and high-to-low temperature shifts on development and growth may not be symmetric. When eggs are reared at 25{degrees}C and then shifted to 17{degrees}C, larval and pupal durations undergo reduction compared to constant 17{degrees}C, but it produces slightly larger adults. A higher egg-stage temperature thus seem to exert a carryover effect that accelerates subsequent development and growth when later stages experience colder temperatures. Surprisingly, flies whose egg stage is exposed to 17{degrees}C followed by a shift to 25{degrees}C also have reduced larval duration and larger size, relative to those developing at constant 25{degrees}C. We speculate this could be either because 17{degrees}C to 25{degrees}C represents a low-to-high temperature shift or a sub-optimal-to-optimal thermal shift that results in metabolic and/or hormonal changes accelerating differentiation and growth. While pupal duration is sensitive to current and to some extent prior thermal environments, it does not contribute substantially to thermal plasticity of size. Development time is longer in males than in females, and this difference seems to start from larval stage while the pupal duration plays a bigger role in creating this sex-specific difference. Overall, employing individual fly rearing, this study helped to unravel the effect of thermal shifts on growth and development in D. melanogaster with great precision.

evolutionary biology↗

bioRxiv2024

Insulin/insulin-like growth factor signaling pathway promotes higher fat storage in Drosophila females

In Drosophila, adult females store more fat than males. While the mechanisms that restrict body fat in males are becoming clearer, less is known about how females achieve higher fat storage. Here, we perform a detailed investigation of the mechanisms that promote higher fat storage in females. We show greater intake of dietary sugar supports higher fat storage due to female-biased remodeling of the fat body lipidome. Dietary sugar stimulates a female-specific increase in Drosophila insulin-like peptide 3 (Dilp3), which acts together with greater peripheral insulin sensitivity to augment insulin/insulin-like growth factor signaling pathway (IIS) activity in adult females. Indeed, Dilp3 overexpression prevented the female-biased decrease in body fat after removal of dietary sugar. Given that adult-specific IIS inhibition caused a female-biased decrease in body fat, our data reveal IIS as a key determinant of female fat storage.

physiology↗

bioRxiv2024

Computational screening of potential AT1R inhibitors from Nigella sativa for diabetic-hypertensive therapy

Hypertension, frequently coexists with Type 2 diabetes mellitus, causes due to Angiotensin II. Inhibiting Angiotensin II by targeting AT1R can potentially improve hypertension-related complications in patients with T2DM. In this study, we perform an in-silico screening based on molecular docking and molecular dynamic of 305 compounds of Nigella sativa against Angiotensin-II Type1 Receptor (AT1R). Molecular docking studies were conducted to investigate the binding affinities of the selected ligands with the target receptor and compared against the Losartan (control drug). Top 5 ligands were selected based on binding affinity. Subsequently, we conducted an ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiling to assess their pharmacokinetic and safety profiles. Our findings revealed two promising ligands Beta-amyrin (CID-73145) and Taraxerol (CID-92097), which exhibited strong binding affinities and favorable pharmacological profiles with no signs of acute toxicity. The molecular dynamic simulations (MD) including RMSD, RMSF, and MMGBSA binding free energy results showed that selected two ligands bind to AT1R more proficiently with good stability over 100 ns. The computational study serves as a foundational basis for subsequent laboratory and clinical research aimed at identifying selective, potent, and less toxic diabetic-hypertensive therapy targeting AT1R. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/610463v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1b3fdf8org.highwire.dtl.DTLVardef@1e6dafforg.highwire.dtl.DTLVardef@133afd0org.highwire.dtl.DTLVardef@5b93c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗