Biology subjects

Sharma, R.

Publications and source records attributed to Sharma, R..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Targeted delivery of niclosamide to FRβ-expressing macrophages with engineered 2-deoxy glucose dendrimer alleviates endometriosis progression and associated hyperalgesia

Endometriosis is a chronic, incurable disease. Due to limited efficacy, high recurrence rates, and serious side effects of current treatments, development of new, targeted, non-hormonal therapies is urgently needed. We previously reported that niclosamide, an FDA-approved anthelmintic drug, attenuates endometriotic lesion growth. We further identified folate receptor-{beta} (FR{beta})-positive macrophages as contributors to disease progression. Significantly, niclosamide inhibits FR{beta}+ macrophages and reduces inflammation, innervation, and angiogenesis. To develop niclosamide as a non-hormonal and selective immune cell-targeted therapy for endometriosis, we engineered a folic acid-conjugated 2-deoxyglucose dendrimer (FA-2DG-D) using click chemistry to enable selective FR{beta}-mediated uptake. Conjugation of niclosamide to FA-2DG-D yielded a targeted nanotherapeutic (FA-2DG-D-Niclo) with enhanced aqueous solubility, controlled intracellular release, and excellent batch-to-batch reproducibility. In a mouse model of endometriosis, FA-2DG-D demonstrated lesion-specific accumulation and selective internalization by FR{beta} macrophages with minimal off-target organ retention. A single intraperitoneal dose of FA-2DG-D-Niclo (25 or 50 mg/kg/bw of niclosamide) significantly reduced FR{beta} macrophage burden, suppressed lesion number and volume, and markedly improved endometriosis-associated hyperalgesia at two weeks post-treatment. Together, these findings establish FR{beta} macrophages as a potential target in endometriosis and present FA-2DG-D-Niclo as a non-hormonal, macrophage-focused nanomedicine for precise and effective endometriosis treatment. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/704463v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@d0101corg.highwire.dtl.DTLVardef@1d1a0bborg.highwire.dtl.DTLVardef@18f9271org.highwire.dtl.DTLVardef@d76bc7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Pharmacokinetics and Physiologically Based Pharmacokinetic Modeling of Mycobacteriophages: Insights into Pulmonary Distribution and Clearance

Bacteriophage therapy is being explored as an alternate therapeutic approach for treating drug- resistant bacteria, including mycobacteria. However, rational phage dosing remains limited by scarce pharmacokinetic (PK) data and an incomplete understanding of tissue distribution. We performed dose-ranging studies in mice of three therapeutic mycobacteriophages (BPs{Delta}, ZoeJ{Delta}, Muddy) after intravenous (IV) and intratracheal (IT) administration. All phages behaved similarly. IV dosing produced biphasic kinetics with non-proportional exposure and declining tissue-to-plasma ratios, indicating saturable uptake and elimination. IT delivery yielded monophasic profiles with [~]390-fold higher lung exposure and [~]490-fold lower plasma exposure, supporting inhaled therapy for pulmonary mycobacterial infections. Using BPs{Delta} data, we developed a mechanistic PBPK model incorporating transcytosis, saturable host clearance, plasma elimination, and lymphatic transport. The model accurately predicted ZoeJ{Delta} and Muddy PK, enabled cross-species extrapolation, and showed that phage morphology influences disposition. This framework advances phage therapy toward model-informed, exposure-guided dose and route selection for multidrug-resistant bacterial infections.

pharmacology and toxicology↗

bioRxiv2026

ST2 Signaling Regulates Innate Immune Responses in Kidney Injury

IntroductionInnate immune cells are critical in inflammation, repair, and fibrosis post-kidney injury. Nuclear-cytokine interleukin (IL)-33, which is released upon tissue damage, signals through IL-1-receptor-like-1 (IL1RL1 or ST2), expressed on many immune cells, including macrophages. However, macrophage regulation by IL-33/ST2 is incompletely understood. We hypothesized that ST2 plays a vital role in activating and/or mobilizing myeloid cells and macrophages to sites of injury. MethodsWe performed acute and chronic ischemia-reperfusion injury (IRI) in mice with myeloid cell-specific deletion of ST2 (ST2fl/fl.LysMCre) to examine the role of myeloid cells ST2 expression in renal injury. The structure and function of the kidney were probed using flow cytometry, histology, immunohistochemistry, quantitative gene expression, and biochemical analysis. The invitro efferocytosis assay, RNA Seq, and Seahorse assay were carried out using bone-marrow-derived macrophages ResultsInterestingly, ST2 deletion resulted in attenuated renal pathology in the acute renal IRI model, whereas in chronic IRI, the loss of ST2 exacerbated kidney injury, suggesting a role of ST2 in the resolution of chronic injury. RNA sequencing (RNASeq) analysis of bone-marrow-derived ST2 sufficient and deficient macrophages showed that loss of ST2 downregulated genes involved in oxidative phosphorylation and clearance of dead cells (efferocytosis). Indeed, the ST2-deficient macrophages had reduced phagocytosis activity. Further, Seahorse analysis revealed that ST2-deficient macrophages had compromised mitochondrial metabolism. ConclusionsWe conclude that the IL-33/ST2 axis is essential for regulating macrophage function and contributes to regulating tissue homeostasis following renal injury.

immunology↗

bioRxiv2026

ISG15 orchestrates dynamic crosstalk between mitochondrial fat oxidation and type 1 interferon in myeloid cells

In contrast to Krebs cycle intermediates, the role of mitochondrial fatty acid oxidation (FAO) in immunometabolism remains incompletely characterized. Studying primary bone marrow-derived macrophages (BMDMs), we show that IFN-{beta} and STING activation augments FAO and associated enzymes carnitine palmitoyltransferase 1a (CPT1a) and acetyl-CoA acetyltransferase 1 (ACAT1). Depleting BMDM Cpt1a reduces FAO and dampens type 1 interferon (IFN) signaling due to decreased histone H3-K9/K14 acetylation, supporting the prior finding of an epigenetic role of FAO in sustaining type 1 IFN. Interestingly, FAO induction by IFN was dynamic as a heightened IFN response suppressed FAO, suggesting a concurrent negative-feedback mechanism. This FAO blunting correlated with increased expression of interferon-stimulated gene 15 (ISG15), a ubiquitin-like modifier known to modulate metabolic proteins through ISGylation. This immune-metabolic signature was similarly operational in mice infected with lymphocytic choriomenigitis virus (LCMV) with temporal discordance between ISG15 levels and FAO. The role of ISG15 in this negative feedback was shown with increased FAO and type 1 IFN response in Isg15 knockout BMDMs. Parallely, endogenous co-immunoprecipitation showed interactions between ISG15 and CPT1a/ACAT1. This ISG15-FAO regulatory interaction was also evident in systemic lupus erythematosus (SLE)-associated interferonopathy and in primary monocytes from SLE individuals that exhibited increased ISG15 levels and reduced FAO rates. Collectively, these findings support a model in which type 1 IFN initially enhances FAO to amplify interferon production, but excessive IFN-signaling induces ISG15-mediated inhibition of FAO, a putative feedback loop that restrains inflammation and preserves immune homeostasis. Together these data identify a novel biphasic FAO-dependent immunometabolic regulatory program. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/700051v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@13f572eorg.highwire.dtl.DTLVardef@174b6aeorg.highwire.dtl.DTLVardef@1856483org.highwire.dtl.DTLVardef@89e5a6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIType 1 IFN rewires myeloid cell metabolism towards FAO. C_LIO_LIFAO epigenetically fuels Type 1 1IFN response. C_LIO_LIEffect of IFN on FAO is dynamic: inducing FAO at low concentrations while suppressing it during a heightened IFN response. C_LIO_LIEnhanced Type 1 IFN response produces ISG15 which ISGylates key enzymes of FAO altering their stability C_LIO_LIISG15 negatively regulates FAO to control Type 1 IFN homeostasis in a negative feedback loop. C_LI

immunology↗

bioRxiv2026

Selective identification of the herb Picrorhiza kurroa and probiotic Lactobacillus fermentum as a synbiotic with fermentation-enhanced physicochemical, biological, and metabolomic properties

PurposeAlthough secondary metabolites of medicinal plants can modulate the gut microbiota, their prebiotic and synbiotic potential is not fully explored. This study aimed to identify novel medicinal plant-probiotic combination(s) that show prebiotic and synbiotic effects through mutual synergism and reciprocal interactions. MethodsTen Himalayan region medicinal plants were screened for their selective prebiotic efficacy by studying in vitro proliferation of three species of lactic acid bacteria (LAB) and concurrent suppression of E. coli. The top-performing plants were evaluated for synergism with LAB through fermentation of pure extracts, followed by physicochemical, biological, and metabolomic profiling. ResultsAmong the ten plant species, Picrorhiza kurroa (PK) and Adhatoda vasica (AV) exhibited promising prebiotic attributes with PAS scores of 0.50 and 0.44, respectively, while Lactobacillus fermentum (LF) emerged as the most compatible probiotic strain. Unlike AV, fermentation of PK with LF demonstrated superior probiotic growth (2.2-fold increase), elevated total flavonoids (21.6% increase), and improved antioxidant capacity (24.02% increase) compared to unfermented PK. Fermented PK significantly enhanced cytoprotective effects and mitigated oxidative (ROS levels/lipid peroxidation) and inflammatory damage (NO/IL-6 levels) in macrophages and muscle cells exposed to separate exogenous stressors (LPS and H2O2). Elemental (ICP-OES) and metabolomic analysis (LC-MS/UHPLC) revealed that LF metabolised major elements of PK (Ca/Fe/K/Na/Cu) and induced biotransformation of large secondary metabolites, including the characteristic iridoid glycosides of PK, into smaller, more abundant metabolites. ConclusionsPK-LF combination is identified as a synbiotic, and its fermented product is a superior bioactive product that can be developed into innovative nutraceuticals or herbal formulations.

biochemistry↗

bioRxiv2026

Root-Suppressed Phenotype of Tomato Rs Mutant is Seemingly Related to Expression of Root-Meristem-Specific Sulfotransferases

Root development and growth are governed by a complex interplay between a plants genetic makeup and its ambient environment. In this study, we characterised a radiation-induced root-suppressed (Rs) mutant mapped on chromosome 4 of tomato. Rs seedlings had a dwarf stature, and mature plants exhibited abnormalities in their leaves, flowers, and fruits. The partial rescue of seedling root elongation by H2S donors or L-cysteine hinted that its root defect is linked to disrupted sulfur metabolism. The metabolite profiling of organs revealed altered homeostasis, analogous to that of plants subjected to sulfur starvation. Whole-genome sequencing revealed that the Rs genome was replete with genetic lesions; therefore, the pleiotropic morphological abnormalities likely emanate from mutations in other genes, including those related to sulfur. Among S-related genes, two sulfotransferase genes (Solyc04g028380 and Solyc04g028390) localised on chromosome 4 showed mutations in their promoters. The expression of both sulfotransferases is confined to the root meristem, suggesting a causal connection with the suppression of root growth. These sulfotransferases belonged to a distinct subset exclusively expressed in the root meristem and were distinct from the tyrosine sulfotransferase involved in the sulfation of root growth factors. Our study suggests that a sulfur-related module, other than tyrosine sulfotransferase, may regulate root development.

plant biology↗

bioRxiv2025

Modeling patient tissues at molecular resolution with Eva

Tissue structure is essential to function and homeostasis in all organs, and disruptions to structure usually indicate disease. Modeling relationships between structural, molecular, and clinical aspects of tissues could advance new diagnostics and treatment strategies. Although profiling techniques like spatial proteomics can capture these relationships, the data remain challenging to extract insight from. Here, we present Eva, a foundation model for tissue imaging data that learns multi-scale spatial representations of tissues at the molecular, cellular, and sample level. Eva uses a novel vision transformer architecture and is pre-trained on masked reconstruction of over 40 million matched spatial proteomics and histopathology images. We show that Eva excels at a variety of tasks, including cross-modal inference from H&E to proteomics stains, quality control, data annotation, zero-shot retrieval, survival modeling, and patient stratification. Extensive evaluations on held-out validation data demonstrate the versatility and generalizability of the learned embeddings. We anticipate that Eva will accelerate translational science by bridging basic research and clinical practice.

bioinformatics↗

bioRxiv2025

HOXA10 is a Temporal Switch in Controlling Decidual Inflammation and Its Dysregulation is Associated with Early Pregnancy Loss

Successful implantation requires precisely timed endometrial inflammation. Although an initial inflammatory burst is essential for implantation, this response must be rapidly resolved for placentation and pregnancy to progress. The mechanisms that coordinate this temporal switch remain poorly understood. Here, we identify the transcription factor HOXA10 as a key regulator of inflammatory transitions in decidual stromal cells and examine how its dysregulation contributes to implantation failure and early pregnancy loss. In mice, HOXA10 expression decreases transiently at implantation and rises again post-implantation. Silencing HOXA10 in human decidualized stromal cells induced a robust pro-inflammatory state, altered integrin and cytoskeletal gene expression, and impaired stromal substrate adhesion. In non-pregnant Hoxa10 hypomorphs, stromal cells exhibited elevated IL1β and TXNIP, activation of the NLRP3/ASC inflammasome, and dysregulation of receptivity markers. During pregnancy, persistent HOXA10 deficiency prevented the resolution of inflammation, resulting in disorganized decidua, defective placentation, infertility, or progressive reproductive decline. To assess translational relevance, we analyzed publicly available bulk and single-cell RNA-seq datasets from first-trimester human decidua and from women with recurrent pregnancy loss (RPL). Single-cell analysis revealed that HOXA10 is selectively low in inflammatory decidual stromal cell clusters, which display concordant upregulation of IL1B, PYCARD, TXNIP, and inflammasome components. Consistently, both bulk and single-cell datasets from women with RPL showed reduced HOXA10 accompanied by increased inflammatory gene expression. Overall, HOXA10 functions as a temporal switch that enables the initial inflammatory activation required for implantation and subsequently suppresses inflammation to support decidual organization, adhesion, and placentation. Loss of this switch leads to persistent decidual inflammation and is associated with pregnancy loss in both mouse models and humans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/691844v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@ee81b6org.highwire.dtl.DTLVardef@85d84eorg.highwire.dtl.DTLVardef@13c1b6aorg.highwire.dtl.DTLVardef@12bed9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Efficient in vivo mammalian neuron editing using peptide-mediated CRISPR enzyme delivery

CRISPR-mediated genome editing of the central nervous system (CNS) has the potential to revolutionize the treatment of neurological disorders, including neurodegenerative disorders such as Huntingtons disease (HD). However, the development of CRISPR therapeutics for the CNS has been hindered by challenges associated with delivery, specifically the lack of a clinically compatible, non-viral delivery technology facilitating genome editing of neurons in vivo. For most indications, two key obstacles must be overcome before therapeutic genome editing of the brain is feasible: non-toxic intracellular delivery of CRISPR cargo into neurons and establishment of strategies enabling targeted brain regions to be edited efficiently. While viral vectors have shown promise in pre-clinical models, non-viral approaches present distinct advantages: ease of manufacture as well as the transient presence of CRISPR machinery, which tempers risks of genotoxicity and immunogenicity. Peptide-enabled ribonucleoprotein (RNP) delivery of CRISPR (PERC) has emerged as a promising non-viral delivery strategy for CRISPR enzymes with initial use in primary human immune cells. In this study, we report the development of Neuro-PERC, a streamlined and optimized approach for in vivo editing of mammalian neurons. Administration of Neuro-PERC reagents via convection-enhanced delivery (CED) mediated efficient and well-tolerated neuronal genome editing. Neuro-PERC enabled robust neuronal editing in the brain of both small and large animal reporter models, and increased survival in a severe murine model of Huntingtons disease. These results establish CED-administered Neuro-PERC as a candidate delivery technology to hasten clinical translation of CRISPR-based therapies for diseases of the CNS. SummaryNeuro-PERC, a peptide-mediated CRISPR enzyme delivery technology, enables efficient in vivo mammalian neuronal editing in the brain of mice and pigs, extending survival in a murine model of Huntingtons disease when administered via convection-enhanced delivery (CED).

neuroscience↗

bioRxiv2025

Deep-Pose-Tracker: a unified model for behavioural studies of Caenorhabditis elegans

Tracking and analyzing animal behaviour is a crucial step in fields such as neuroscience and developmental biology. Behavioural studies in the nematode C. elegans, for example, help in understanding how organisms respond to external cues and how the specific physiological responses link to either instantaneous or learned behaviours. Although tracking behaviour through locomotion patterns and postural dynamics is routine, it becomes laborious and time-consuming when performed manually. Automation of this process is therefore crucial for accurate and fast detection and analysis. To this end, we report Deep-Pose-Tracker (DPT), a YOLO (You Only Look Once)-based model for automated pose detection of C. elegans from videos and images. The module is further utilized for several downstream analysis algorithms to quantify essential behavioural features, including locomotion speed, orientation, forward or reverse locomotion, and complex body bends such as omega turns. In addition, it includes eigenworms decomposition to represent complex posture dynamics in a low-dimensional space. The model shows reliable performance on the validation and test datasets, with high inference speed, while being user-friendly. DPT, therefore, can be a valuable toolkit for automated behavioural quantification of C. elegans under varying experimental stimuli.

animal behavior and cognition↗

bioRxiv2025

A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy

The retinal pigment epithelium (RPE) sustains lifelong proteostasis under chronic stress, yet how post-mitotic cells activate autophagy when canonical kinase pathways suppress it remains unresolved. Here we demonstrate that AKT1, conventionally regarded as an autophagy suppressor, drives autophagy through a non-canonical transcriptional mechanism triggered by isoform imbalance. In RPE and age-related macular degeneration (AMD) models, AKT2 hyperactivation destabilizes mTORC2 and engages S6K-mediated IRS-1 inhibition, creating a feedforward autophagic arrest. Compensatory AKT1 activation via mTORC2 phosphorylates telomerase reverse transcriptase (TERT) at Serine 824, driving nuclear translocation that is independent of telomere maintenance. In the nucleus, TERT assembles with FOXO3 and MYC into a tripartite transcriptional complex that occupies the EIF2AK3 promoter, enabling PERK transcriptional activation. This activity converts the unfolded protein response from pro-apoptotic to cytoprotective: PERK-ATF4 signaling drives biogenesis of core autophagy machinery while simultaneously inducing selective ERphagy through the receptors TEX264 and CCPG1, which prevents pathological PERK clustering and preserves tubular ER architecture in diseased RPE. Using C. elegans phosphorylation-deficient mutants, mouse models and AMD patient induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE), we establish that AKT1-mediated TERT phosphorylation is an evolutionarily conserved prerequisite for FOXO/DAF-16 nuclear function and lysosomal homeostasis in post-mitotic cells. Pharmacologic targeting of AKT2 with a first-in-class dual-pocket allosteric inhibitor selectively enhances AKT1 compensation, restoring macroautophagic and ERphagy flux across disease models. These findings reveal a kinase-to-transcription axis that reprograms organelle quality control and identify the AKT1-TERT-PERK-ATF4 pathway as a therapeutic target in proteostasis-driven disease.

cell biology↗

bioRxiv2025

Community coalescence reveals strong selection and coexistence within species in complex microbial communities

Complex microbial ecosystems harbor extensive intra-species diversity, but the fitness consequences of this genetic variation are poorly understood in community settings. Here we address this question by competing in vitro gut communities derived from different human donors, revealing the emergent fitness differences between conspecific strains as they competed within larger communities. Most pairs of strains experienced strong and context-dependent selection, even when their parent communities were originally selected in the same nutrient environment. However, these fitness differences typically attenuated over time due to biotic interactions within the community, leading to extended coexistence within many species, and competitive exclusion in others. These results support the view that conspecific strains can fulfill distinct ecological roles when competing within a diverse community, even when their genomic diversity exhibits the hallmarks of a single biological species.

evolutionary biology↗

bioRxiv2025

Bone Resists Fatigue Through Crack Deceleration at the Fibril Scale

Bone endures millions of cycles throughout its lifetime by accumulating damage at a rate slow enough to allow for cell-mediated repair, but the mechanisms that delay this fatigue failure remain poorly understood. While prior studies have focused on the fatigue response of macroscale architecture of bone, the role of its nanoscale structure in resisting fatigue has been experimentally inaccessible. Here, we combine in-situ fatigue loading with synchrotron X-ray tomography and radiography to directly observe crack propagation in human bone with [~] 21 nm spatial and 100 ms temporal resolution. We find that mineralized collagen fibrils decelerate crack growth through branching along the fibril axes, while orthogonal cracks are intermittently decelerated by nanoscale interfibrillar interfaces. These mechanisms suppress damage accumulation under physiological loads by an order of magnitude. Our findings uncover a previously unobserved toughening strategy at the nanoscale, providing insight as to how the hierarchical structure of bone bridges the timescale gap between mechanical damage and biological repair.

bioengineering↗

bioRxiv2025

RAB14-dependent tubulovesicular recycling directs MET to invadopodia promoting TNBC cell invasion

Metastasis is one of the primary causes of cancer-related death in Triple-negative breast cancer patients. During metastatic dissemination, the cancer cells infiltrate in to surrounding tissue employing specialized membrane-protrusion with proteolytic activity called invadopodia. Cues from growth factors via the cognate receptor tyrosine kinases promote invadopodia formation and cancer cell invasion. We report the role of HGF and its cognate receptor MET in TNBC invasion. The results from our study demonstrate that the TNBC cells when stimulated with HGF promotes invadopodia formation and facilitates delivery of MT1-MMP to the invadopodia in a MET dependent manner. We also showed that MET resides at invadopodia and its localization at invadopodia increases upon HGF treatment due to enhanced surface delivery of the RTK. By employing a degradation defective mutant, we demonstrated the critical role of MET recycling in driving breast cancer invasion. Moreover, we observed that the RCP-RAB14 axis mediates the surface delivery of MET through tubulovesicular carriers, with KIF16B promoting the formation of vesicular tubules on RAB14-positive endosomes. Collectively, the study provides mechanistic insights on the growth factor-mediated recycling of RTK and the associated metalloprotease in invadopodia-dependent matrix degradation and cancer cell invasion.

cancer biology↗

bioRxiv2025

Multiple Epigenetic Mechanisms Functionally Cooperate to Silence Expression of Somatostatin Receptor Type 2 in Pancreatic Neuroendocrine Tumors

Pancreatic neuroendocrine tumors (PNETs) are a rare and understudied set of cancers, with increasing incidence. Neuroendocrine tumors are unique in the fact that they express high levels of the somatostatin receptor type 2 (SSTR2), which represents a target for both tumor imaging and therapeutics. PNET grade inversely correlates with SSTR2 tumor staining and higher tumor grade is associated with poor patient prognosis. With no known mutations, SSTR2 expression is believed to be lost through aberrant epigenetic mechanisms. Enhanced knowledge of the epigenetic biology and players controlling SSTR2 expression may allow for identification of novel PNET imaging and treatment modalities. Through in-depth studies, we found that the specific de novo DNA methyltransferase (DNMT), DNMT3B, is responsible for SSTR2 gene CpG methylation and silencing. Using DNMT3B as a starting point, along with the concept of functional crosstalk between various epigenetic mechanisms, we further discovered that Polycomb Repressor Complexes 1 and 2 (PRC1 and PRC2) play important roles in silencing SSTR2. Moreover, we found several histone lysine demethylases, enzymes that remove activating histone H3K4 methylation marks, to be critical for silencing expression of SSTR2. We additionally identified several chromatin remodeling enzymes/complexes as cellular factors that negatively regulate SSTR2 expression. Finally, using the HiBiT luminescent reporter system, we exploited functional chemo-genomic screens to further expand our knowledge of SSTR2 epigenetic control. These screens both reinforced several of our initial findings and helped to identify additional silencing mechanism potentially regulating SSTR2 expression. A commonality in our findings point to the presence, or necessity, of Class I HDACs in nearly all the epigenetic silencing mechanisms characterized. Overall, our work demonstrates that SSTR2 gene expression is likely silenced through various dynamic and interconnected epigenetic events, resulting in a compacted, transcriptionally repressed chromatin environment. Our study offers novel potential therapeutic targets and combinations to best increase expression of SSTR2, which are currently being tested in pre-clinical studies from our group, with the goal of future clinical trials aimed at increasing SSTR2 expression in high-grade, SSTR2-low NET patients.

cancer biology↗

bioRxiv2025

Comprehensive healthspan assessments and influence of sex as a biological variable in aging rats

Rats share a significant amount of genetic and physiological similarity with humans. Many biological processes and pathways are conserved between rats and humans, making rats a suitable model for studying various aspects of human health and disease. Using rats as an aging model offers a more ethical alternative to using larger, longer-lived animals like primates. Rats are easier to handle in laboratory settings, as compared to non-human primates, both of which have physiological functions like humans. To date, there are very few studies which have comprehensively studied age-related changes in rat physiology. Here we present a longitudinal assessment of several aspects of Brown-Norway rat physiology and histopathology using molecular and functional assessments at 6-, 17- and 27 months of age. Our studies thus provide age-related healthspan parameters, which can be used as reference for genetic or pharmacological rat models of aging.

animal behavior and cognition↗

bioRxiv2025

Exhausted-like effector CD8 T cells mediate immune-stromal interactions at mucosal Chronic Graft-versus-Host Disease onset

Chronic graft-versus-host disease (cGVHD) frequently follows allogeneic hematopoietic stem cell transplantation and impacts the mucosa. This atlas study highlights the role of exhausted-like effector CD8+ T cells (TEXEF) in oral mucosal cGVHD pathogenesis. Biopsies from the oral mucosa were collected at oral cGVHD onset or at six months post-transplant and analyzed using single-cell RNA sequencing and other modalities. At cGVHD onset, in addition to changes in the myeloid compartment, two distinct populations of CD8+T cells with a TEXEF phenotype were prevalent: an inflammatory CD8T cell cluster (CD8T_4) expressing CCL4, CD69, and TNFSF9, and an exhausted CD8T cell cluster (CD8T_5) characterized by the expression of CXCL13, HIF1A, and HLA-DRA, both correlated with clinical disease severity. Pseudo-time analysis suggests a transition from the inflammatory pre-exhausted CD8T_4 cluster to the cytolytic, terminally exhausted CD8T_5 cluster. The CXCL9-CXCR3 interactions among CD8+ T cells, fibroblasts and myeloid cells are implicated in tissue damage. Onset of cGVHD despite frequent oral mucosal FOXP3 regulatory CD4T cells suggests potential impaired Treg function or CD8+T cell dysfunction. These findings highlight TEXEF cells as key contributors to oral cGVHD pathology and potential therapeutic targets for mitigating sustained tissue injury in cGVHD.

immunology↗

bioRxiv2025

From Photoperiod Thresholds to Photoperiod sensitivity: Dual Strategies for Cost-Effective Speed Breeding and Climate-Ready Barley

Yield and the duration of the growing season are closely linked. Climate change may shorten growing seasons in certain European regions, and reducing the time to flowering could be an effective strategy to mitigate its effects. Therefore, exploring allelic combinations shape flowering time, is needed. Additionally, speed breeding (SB), characterized by extended photoperiods to accelerate generation time, can be energy-intensive, and the shortest day length needed to induce rapid flowering remains unknown. We present the first integrated study of how allelic variation at three key flowering time genes, PPD-H1, ELF3 and PHYC, modulates three parameters of the photoperiod response model: threshold photoperiod, photoperiod sensitivity, and intrinsic earliness. We recorded flowering under lengths of 16-24h in Near Isogenic Lines carrying PhyC-e or PhyC-I allele within ppd-H1 background, and in lines from HEB-25 combining wild and domesticated alleles of ELF3 and PPD-H1. The ELF3 allele in ppd-H1 background reduced intrinsic earliness, whereas PhyC-e reduced photoperiod sensitivity, opening opportunities for climate change adaptation. Remarkably, ppd-H1 lines flowered at a 20-h threshold, whereas Ppd-H1 lines showed no response, consequently we propose new SB photoperiods at 20 and 16h depending on PPD-H1 background. These photoperiods lower energy costs compared to the current 22h standard. HighlightsBy studying barley key photoperiod response genes, our results support energy-efficient speed breeding and the development of climate-resilient varieties through targeted genetic control of flowering time.

plant biology↗