Biology subjects

Ibrahim, M.

Publications and source records attributed to Ibrahim, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Behavioral dysfunction but not wasting in cancer cachexia is driven by altered tryptophan metabolism

Cancer cachexia causes pathological weight loss, anorexia, and depressive symptoms, culminating in increased mortality. Using mouse models of pancreatic cancer cachexia, we identify tumor and hepatic inflammatory signaling, multi-organ energy charge depletion, and altered tryptophan metabolism. Metabolomic profiling and stable isotope tracing revealed altered tryptophan fates: serotonin depletion and kynurenine accumulation across tumor, liver, muscle and spleen. Kynurenine accumulation involved accelerated conversion of tryptophan to kynurenine with slowed downstream conversion to kynurenic acid. Restoring serotonin activity pharmacologically or metabolically normalized feeding, locomotion, and depression-like behavior, but wasting, tumor burden, and survival remained unchanged. Blocking kynurenine production or kynurenine-mediated AhR activation pharmacologically produced similar results. Thus, in cancer cachexia, the tryptophan pathway is subverted to deplete serotonin and accumulate kynurenine. This subversion contributes to cachexia-associated behavioral and feeding defects but not lethal systemic catabolism.

cancer biology↗

bioRxiv2026

Engaging the host adaptive response to nutrient limitation delays cancer cachexia

Cancer cachexia is a debilitating wasting syndrome associated with involuntary weight loss, reduced appetite and food intake, adipose and muscle atrophy, and systemic inflammation with induction of a myriad of candidate cachexia factors. Using a multi-omic approach in a genetically engineered mouse model of lung cancer cachexia, we found that early circulating metabolic alterations preceded overt weight loss. Although both cachexia and fasting are characterized by a reduction in food intake, we show that the systemic metabolic changes in cachexia are distinct, indicating a lack of induction in the normal protective response to negative energy balance during cachexia. Cancer cachexia causes profound hepatic reprogramming, and activation of inflammatory programs, alongside muscle atrophy and elevation of circulating cytokines. However, targeting individual candidate cachectic factors such as IL-6, TNF-, GDF15, CCL2, LIF, and IL17A failed to rescue weight loss or prolong survival. In contrast, caloric restriction initiated prior to tumor induction elicited a program of protection during tumor progression that attenuated multi-tissue inflammatory and catabolic transcriptional responses, preserved lean mass, and prolonged survival. Together, these findings suggest that metabolic preconditioning broadly dampens systemic inflammation and delays the onset and progression of cancer cachexia.

cancer biology↗

bioRxiv2026

Cross-species spatial profiling links progranulin to an immune suppressive niche in brain metastasis

Immune checkpoint inhibitors (ICI) have revolutionized the treatment of brain metastasis (BM), demonstrating intracranial response rates and durability not previously seen with other therapies. However, approximately 50% of patients do not respond to ICI, and the brain-specific interactions that shape anti-tumor immunity remain poorly understood. We profiled five syngeneic BM models using spatial transcriptomics, identifying myeloid-rich niches enriched for interferon-responsive and disease-associated microglia (DAM)-like programs. Ligand-receptor colocalization analyses identified progranulin (PGRN) as a candidate mediator of these niches. Host- or tumor-cell Grn loss reduced BM burden, and Grn-deficient macrophages exhibited altered metabolic programs and tumor-cell engulfment in vitro. Across independent human BM datasets, GRN expression was associated with conserved lysosomal and DAM-like myeloid programs, and GRN-high myeloid regions colocalized with immunosuppressive signatures and dysfunctional CD8+ T cell states. These cross-species findings identify PGRN as a candidate mediator of the BM immune niche and support further investigation of its therapeutic relevance.

cancer biology↗

bioRxiv2026

Decoding Tumour-Specific Rewiring and Synthetic Lethality Through Genome-Scale Metabolic Models

Cancer cells rapidly rewire their metabolism, from efficient energy production toward anabolic processes, to sustain uncontrolled growth. Decoding such metabolic shifts is essential for uncovering novel therapeutic targets. To map systems-level metabolic changes across cancer types, we built context-specific genome-scale metabolic models for eight tissues (lung, thyroid, stomach, prostate, liver, kidney, colon, and breast) using gene expression data from The Cancer Genome Atlas (TCGA). Applying constraint-based modelling, we then identified differentially regulated pathways through flux enrichment analysis, revealing tissue-specific rewiring: branched chain amino acid metabolism was suppressed in breast cancer; sphingolipid metabolism was downregulated in colon, kidney, and thyroid but upregulated in breast. We further propose a model-driven pipeline to identify and characterise metabolic vulnerabilities. We first identify synthetic lethal reactions in normal tissues and their corresponding single lethal counterparts in cancers, thereby enabling the identification of metabolic "collateral lethal" reaction pairs for each cancer. Model-predicted collateral lethal gene pairs, including CMPK1-AK in colon, ALDOA-PGD in prostate, and SLC25A26-UQCRB in liver models, were supported through computational validation using DepMap data on gene essentiality. Subsequently, we show how to interpret metabolic rewiring in cancer tissues while accounting for any collateral lethal pairs. In summary, our results establish a systemic framework for decoding metabolic rewiring and synthetic lethal vulnerabilities in cancer.

systems biology↗

bioRxiv2026

Systematic assessment of the biological impact of cellular deconvolution on downstream analyses of disease transcriptomes

Background Cellular deconvolution methods estimate cell type proportions from bulk RNA seq data, typically using single cell RNA seq derived signatures, enabling separation of disease associated transcriptional changes into composition driven and cell intrinsic effects. However, these approaches depend on model assumptions and the stability of cell type signatures, and it remains unclear how deconvolution related uncertainties influence downstream analyses and biological conclusions. Results We systematically evaluated the effect of cell type correction on disease relevant transcriptomic insights, using Alzheimer's disease (AD) as a model and the Mount Sinai Brain Bank cohort as a primary dataset. Applying dtangle, selected after comparison with another deconvolution approach, we estimated cell type proportions across four brain regions and assessed how correction reshaped differential gene expression and pathway enrichment. Cell type correction (CTC) markedly altered differentially expressed gene (DEG) profiles in a region dependent manner: the superior temporal gyrus lost all significant signals, while the frontal pole gained DEGs with improved cross region concordance. At the pathway level, correction shifted enrichment from synaptic loss and immune activation toward suppression of stress response and immune regulatory programs, suggesting that composition changes partly obscure cell intrinsic regulatory signals. Overlap with AD genome wide association study loci and replication in an independent cohort indicated that cell intrinsic changes are more consistently validated than composition driven changes. Notably, KCNN2 and RIMS1, not currently recognized as canonical AD biomarkers, emerged as robust transcriptional signatures, potentially reflecting both compositiondriven and cell intrinsic dysregulation and warranting further investigation. Conclusions Parallel evaluation of uncorrected and CTC analyses distinguishes composition driven from cell intrinsic transcriptional effects and highlights robust disease signatures in heterogeneous tissues such as the brain.

bioinformatics↗

bioRxiv2026

Endogenous APOBEC3B Promotes CHK1 Inhibitor Sensitivity

APOBEC3B (A3B) is a single-stranded DNA cytosine deaminase overexpressed in cancer, where it causes genomic DNA damage and mutations associated with tumor evolution. Enforced A3B overexpression triggers a dependency on the replication-stress response in different cellular models. However, whether endogenous A3B in cancer cells might yield a similar vulnerability is unclear. Here, we investigate how endogenous A3B expression and catalytic activity affect sensitivity to CHK1 inhibition, using two cancer cell lines, JHOC5 and U2OS. A3B-expressing cancer cells are sensitive to two chemically distinct CHK1 inhibitors, GDC-0575 and Prexasertib. CHK1 inhibitor sensitivity is reduced by A3B CRISPR knockout and restored by re-expressing wildtype A3B in knockout cells. Moreover, an endogenous A3B-E255A catalytic mutant generated by homology-directed repair phenocopies the reduced CHK1 inhibitor sensitivity of A3B-null cells, demonstrating a DNA deamination-dependent mechanism. CHK1 inhibition induces replication-associated DNA damage and cell-cycle perturbation dependent on A3B expression. As a result, A3B-expressing cells accumulate more pan-nuclear {gamma}H2AX, aberrant DNA-content profiles, and an expanded EdU-negative S-phase population, which are hallmarks of stalled DNA replication. In comparison, A3B-null and A3B-E255A cells retain defined cell-cycle distributions and are less sensitive to CHK1 inhibition. Together, these findings identify endogenous A3B-catalyzed deamination as a therapeutically actionable source of replication-associated DNA damage that renders tumor cells selectively dependent on CHK1 function. Statement of significanceAPOBEC3B causes mutations in cancer cells and simultaneously imposes DNA replication stress. This combines to sensitize tumor cells to chemical inhibitors of the DNA damage response kinase CHK1.

cancer biology↗

bioRxiv2026

Autoantibodies Drive Fc Gamma Receptor-Dependent Colon Inflammation During Immune Checkpoint Blockade

Immune checkpoint inhibitor (ICI)-associated colitis limits effective cancer immunotherapy, yet host determinants of severe toxicity remain undefined. We investigated whether humoral immunity is associated with subsequent severe immune-related colitis (irC). In melanoma patients, baseline serum autoantibody (AAb) profiling identified a composite antigen signature - a signature-level association rather than validated functional specificities - associated with severe irC, marked by retained reactivity to tumor-associated antigens and relative depletion of antibodies recognizing immune- and mucosal-regulatory proteins. To assess functional relevance, we transferred polyclonal IgG from severe- or non-severe-irC patients into wild-type or humanized Fc{gamma} receptor (hFc{gamma}R) mice treated with anti-PD-1 or anti-CTLA-4. IgG alone did not induce inflammation; however, severe-irC IgG amplified checkpoint-driven colonic inflammation in hFc{gamma}R mice, but not in wild-type mice, with checkpoint-specific remodeling of myeloid, lymphoid, and innate lymphoid compartments. These findings suggest that pretreatment humoral immunity conditions susceptibility to irC via the IgG-Fc{gamma}R axis.

cancer biology↗

bioRxiv2026

Short T1 Fraction as a Marker of Myelin Content: Evidence from Postmortem MRI and Histology

PurposeTo investigate the short-T1 fraction as a potential biomarker of white matter myelin integrity, using myelin histology as ground truth. MethodsMulti-inversion-time MRI data were acquired from four postmortem brain hemisphere specimens from donors with Alzheimers disease on a clinical 3T scanner, and from five dissected tissue blocks containing white matter hyperintensities (WMHs) on a preclinical 3T system. Short-T1 fraction maps were generated using inverse Laplace transform to isolate short-T1 components and were compared with T2-based myelin water imaging metrics through joint T1-T2 correlation analysis. Short-T1 fraction maps from the tissue blocks were further compared with myelin-stained histology. In addition, in vivo short-T1 fraction data were acquired from two elderly volunteers with WMHs to demonstrate translational feasibility. ResultsPostmortem MRI revealed reduced short-T1 fractions in WMHs. T1-T2 correlation analysis showed that the short-T1 fraction was closely associated with the short-T2 (myelin water) component. Strong correlations were observed between short-T1 fractions and optical densities from both Luxol Fast Blue- and myelin basic protein-stained histological sections, supporting the link between the short-T1 signal and myelin content. Consistent findings were also observed in vivo, where significant reductions in short-T1 fractions were detected within WMHs. ConclusionThe short-T1 fraction correlated with myelin content in postmortem brain white matter, supporting its potential as a clinically translatable biomarker of myelin integrity.

neuroscience↗

bioRxiv2026

STING dampens the unfolded protein response to enable the presentation of self-antigens on MHC-I during inflammation.

A growing body of evidence supports the contribution of the long-lasting adaptive immune system in Parkinsons disease (PD). We showed that the PD-associated protein PINK1 negatively regulates the presentation of mitochondrial antigens (MitAP) on MHC-I molecules. In vivo evidence indicated that MitAP activation in mice, in the absence of PINK1, led to cytotoxic CD8+ T cell stimulation and severe motor impairments, reversible by L-DOPA. We show here that following TLR4 activation, MitAP is engaged through a pathway involving cGAS-STING, which acts as a rheostat to dampen the unfolded protein response (UPR). Without STING, the stress response is amplified, leading to a translational attenuation that inhibits the expression of XBP1s, a transcription factor required for MitAP. STING activity also regulates the repertoire of peptides displayed at the cell surface during inflammation, highlighting a potential role in immunosurveillance. These findings establish STING and the UPR as key immune regulators targetable for therapeutic intervention during autoimmune diseases and PD.

immunology↗

bioRxiv2026

Lymphatic egress recycles tumor-experienced effector CD8 T cells to sustain immune surveillance

Successful anti-tumor immune surveillance depends on stem-like CD8+ T cells that are enriched in tumor-draining lymph nodes (LN), but how they are maintained over time remains poorly understood. Here, we identify a continuous lymphatic circuit that sustains stem-like CD8+ T cells. Using photoconversion to fate-map intratumoral T cells we demonstrate that effector cells exit the tumor microenvironment and migrate back to the draining LN. These tumor-specific, migratory effector T cells avoid chronic antigen stimulation, re-express the transcription factor associated with self-renewal, TCF1, and enter a stem-like state in the LN. Antigen presentation in LNs by dendritic cells drives their proliferation thereby inflating the LN stem-like population. Consequently, maintenance of stem-like T cells and ICB response depends on constitutive lymphatic transport, while LN metastasis compromises the stem-like niche, diminishing ICB response. We, therefore, define a continuous, peripheral lymphatic circuit that recycles tumor-experienced effector T cells to fuel durable, systemic immune surveillance.

immunology↗

bioRxiv2026

Ant abaecin-2 is a context-dependent copper-binding effector that can be either inhibitory or protective

Host defense peptides (HDPs) are important components of the innate immune system that are used to combat pathogens and often rely on metal binding for their function. However, controlling trace nutrients such as transition metals may have other roles in host-symbiont interactions beyond poisoning harmful pathogens. This study characterizes the evolution, structural properties, and biochemical activity of the novel hymenopteran HDP abaecin-2. In myrmicine ants such as the fungus-growing tribe Attini, abaecin-2 has evolved to include an Amino-Terminal Cu(II) and Ni(II)-binding (ATCUN) motif, which we hypothesize may bind copper, a trace nutrient that is enriched in attine ant colonies. Combined results from mass spectrometry, competitive binding assays, circular dichroism, and NMR indicate that the abaecin-2 peptide lacks a defined secondary structure and can associate with up to 2 Cu(II) ions, one strongly bound at the ATCUN motif and another weakly bound, likely at a conserved histidine residue. Despite its copper-binding activity, abaecin-2 alone does not exhibit antibacterial activity against Escherichia coli or Bacillus subtilis (models for bacteria that live in ant fungus gardens). However, it synergizes with a model pore-forming peptide cecropin A to inhibit the growth of E. coli, similar to the related peptide abaecin-1. The copper-binding activity conferred by the ATCUN motif also protects copper-sensitive E. coli from excess copper toxicity. The dual, context-dependent inhibitory and protective roles we propose for abaecin-2 indicate that this previously under-characterized HDP may be used by attine ants to regulate both harmful and beneficial symbionts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/719391v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1298f41org.highwire.dtl.DTLVardef@17c16d9org.highwire.dtl.DTLVardef@1c03081org.highwire.dtl.DTLVardef@b0a5a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination

Phenotypic plasticity is a prominent cancer feature that contributes to metastatic potential and resistance to therapy across multiple cancer types. Cancer cell state transitions have been attributed to transcriptional programs, such as the AP1/TEAD-regulated gene network driving the mesenchymal-like (MES) phenotype. In addition, during dissemination, tumor cells are subjected to variable loads of physical mechanical pressure and constriction across transited tissue, which are thought to impact nuclear molecular crowding. How the interplay between mechanical pressure, global 3D nuclear architecture and transcriptional programs contributes to MES identity and metastatic adaptation remains unclear. Using cutaneous melanoma as a model for early dissemination, we integrate in vitro and in vivo epigenomic profiling with nanoscale imaging of cell lines and patient samples to investigate chromatin organization features underlying the MES phenotype. We find that in MES cells, CTCF is relocated from domain boundaries to regulatory regions of EMT-like genes, leading to reduced insulation, extended topological associated domains (TADs) and increased inter-domain contacts, and de novo formation of chromatin hubs. This conformational rewiring, along with loss of heterochromatin, supports nuclear deformability during invasion and dissemination. Conversely, physical constriction of melanocytic cells induces MES-like chromatin features--including CTCF repositioning and heterochromatin loss-- and promotes metastasis in vivo. Similarly, pharmacological inhibition of the heterochromatin mark H3K9me3 triggers MES characteristics and increases invasiveness. These results demonstrate that metastatic competency involves both epigenetic and structural nuclear reprogramming, enabling shifts in gene networks and physical adaptability. Our findings reveal mechanistic links between nuclear architecture and aggressive tumor behavior, identifying potential biomarkers and therapeutic targets to intercept metastatic progression.

cancer biology↗

bioRxiv2026

NF1 Loss Remodels Tumor Niches for Immune Evasion

Genetic and transcriptional alterations in cancer cells shape their interactions with immune and stromal compartments, influencing tumor progression, immune evasion, and response to immune checkpoint inhibitors (ICI). Yet, how these interactions are organized within tumor architecture and linked to clinical outcomes remains unclear. Neurofibromin 1 (NF1) is a tumor suppressor gene that is frequently inactivated across multiple cancer types. NF1 loss-of-function mutations occur in up to 27% of melanoma cases and are associated with poor clinical outcomes. Here, we used spatial multi-omics analysis to uncover 12 meta-niches, each comprising distinctive cell types with distinct characteristics, in human melanoma tissues. We found that niches containing immunosuppressive cancer-associated fibroblasts (CAFs) and macrophages were significantly enriched in NF1 mutant melanoma (NF1Mut) tissues. In contrast, niches containing cytotoxic CD8 T cells were significantly diminished. NF1 loss correlates with increased epidermal growth factor signaling (EGFR) signaling and reduced antigen presentation in tissues with limited CD8 T cell infiltration in both human and mouse melanoma. We demonstrate that EGFR inhibition restores antigen presentation and activates immune responses in a syngeneic Nf1 knockdown model resistant to ICIs. These data, therefore, define functionally distinctive niches enriched in NF1Mut melanoma that likely contribute to their aggressive nature and nominate EGFR signaling as a specific target to reinvigorate ICI responses. We therefore link an understudied genetic driver to specific immune architectures and ultimately therapy resistance and suggest a therapeutic strategy expected to improve treatment outcomes in NF1Mut melanoma patients.

cancer biology↗

bioRxiv2025

RNA at Lipid/Water Interfaces: Molecular Insights from Coarse-Grained Simulations and Reflectivity Data Predictions

Interactions between RNA and lipids are fundamental for biological processes and are increasingly exploited for RNA delivery by lipid nanoparticles. However, RNA-lipid interactions remain challenging to characterize at the molecular level. Here, we address the modeling of RNA at lipid/water interfaces using coarse-grained (CG) simulations, experimental validation using scattering data and prediction of neutron (NR) and X-ray reflectivity (XRR) profiles from the simulations. Using neutral DOPC and cationic DOTAP bilayers, we show that lipid-RNA interactions depend strongly on RNA secondary structure, with single-stranded regions exhibiting higher interfacial affinity than double-stranded segments. We validate the CG lipid simulations, showing that while they reproduce experimental X-ray scattering data only qualitatively, the agreement improves markedly after backmap-ping to atomistic resolution followed by energy minimization and short all-atom molecular dynamics simulations. We further simulated distinct tRNA conformations and analyzed the influence of RNA secondary structure, concentration, solvent contrast, and lipid deuteration on NR and XRR signals identifying the conditions under which such experiments probe RNA adsorption and discriminate between different RNA conformations. Together, these results demonstrate that CG simulations combined with reflectivity data provide a powerful approach to probe RNA adsorption and structure at lipid/water interfaces and support the design and interpretation of scattering experiments. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/689668v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@9a1297org.highwire.dtl.DTLVardef@13aa90dorg.highwire.dtl.DTLVardef@30a68corg.highwire.dtl.DTLVardef@662aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B

The single-stranded DNA deaminase APOBEC3B (A3B) is capable of potently restricting the replication of a range of viruses including retroviruses (cDNA) and herpesviruses (genomic DNA). However, these and likely other DNA virus families have evolved host species-specific counter-defenses that are equally potent and serve to protect viral DNA from restriction. Although high-risk human papillomavirus (HPV) infection triggers A3B upregulation, potentially as part of an antiviral response, the impact of this restriction factor on papillomavirus replication and pathogenesis has yet to be assessed. To study human A3B antiviral function in the absence of a species-specific counter-defense, here we ask whether human A3B is capable of restricting Mus musculus papillomavirus (MmuPV1) in cellulo and in vivo. First, we created human A3B and catalytic mutant A3B-E255A expressing FVB/N mice. Second, MmuPV1 gene expression and replication was quantified in primary keratinocytes from these animals and, surprisingly, enzymatically active human A3B caused no measurable impairment in viral transcript or DNA accumulation. Third, A3B, catalytic mutant A3B-E255A, and nontransgenic FVB/N animals were infected with MmuPV1 and similar pathologies were found regardless of A3B functionality. Thus, despite likely never being exposed to human A3B during evolution, MmuPV1 appears to be unaffected by this potent, primate-specific antiviral factor. These results suggest that MmuPV1 and perhaps papillomaviruses more broadly possess a conserved mechanism to efficiently escape restriction by human A3B and related DNA deaminases. IMPORTANCEHuman papillomaviruses (HPVs) are nearly ubiquitous, and persistent infection with high-risk types causes approximately 5% of cancers worldwide. Although HPV vaccination is effective for preventing infection, insufficient global coverage and a rising incidence of HPV-associated malignancies, such as oropharyngeal carcinoma, highlight the need to understand innate virus clearance mechanisms. APOBEC3 enzymes are a central component of the mammalian innate immune system and are hypothesized to restrict papillomavirus infection, particularly between species. Here, we establish mice that express the human antiviral enzyme APOBEC3B (A3B). Surprisingly, we find that human A3B is incapable of blocking the replication of a murine papillomavirus (Mus musculus papillomavirus 1, MmuPV1) in relevant primary cells from these animals or in infected tissues in vivo. These findings highlight the complexity of teasing apart host-pathogen interactions and suggest that papillomaviruses may have a general mechanism for escaping restriction by antiviral enzymes such as A3B.

microbiology↗

bioRxiv2025

Exploring Cerebellar Hippocampal Dynamics in Temporal Lobe Epilepsy: A Multivariable Synthetic Modeling Study of Purkinje Cell Degeneration and Stimulation Timing

ObjectiveTo investigate whether Purkinje cell degeneration precedes or follows seizure onset in temporal lobe epilepsy (TLE), delineate shared cerebello-hippocampal pathways, and assess the influence of stimulation timing on modeled seizure outcomes. MethodsWe developed a comprehensive 50-variable evidence model integrating structural, molecular, and circuit-level variables sourced from existing literature. Utilizing this framework, we created a PASS-validated (see Appendix for details)synthetic cohort comprising 10,000 virtual subjects. Analytical approaches included causal inference via inverse probability of treatment weighting (IPTW), mediation analysis, factorial ANOVA, and equivalence testing using the Two One-Sided Test (TOST). The models predictive fit was intentionally modest (RMSE = 0.499; R2 = -0.010), aligning with its primary role in causal exploration rather than precise outcome forecasting. Statistical evaluations were stratified by timing and circuit integrity factors. ResultsCausal reanalysis indicated that Purkinje cell density exerted a weak, nonsignificant direct effect on seizure burden (average treatment effect [ATE] = +0.0045, 95% CI: -0.0053 to +0.0143) (see Table 1, row 1). Mediation analysis revealed negligible indirect effects through GABAergic modulation pathways. In contrast, stimulation timing proved a pivotal factor: early intervention ([≤]4 days post-onset) resulted in significantly enhanced seizure reduction (p = 0.045, mean {Delta} = -0.020), accompanied by a notable timing x integrity interaction (Table 1, row 3). Factorial ANOVA substantiated this interaction (F = 3.30, p = 0.019, partial 2 = 0.001), with Tukeys honest significant difference (HSD) post-hoc tests identifying timing as the primary differentiator. Equivalence testing via TOST, using a predefined margin of {+/-}0.015 seizures/hour, did not fully establish equivalence for Purkinje effects (p1 = 0.0019, p2 = 0.136), though the confidence interval suggested minimal clinical relevance. Sensitivity analyses, including outlier assessments and biological noise simulations, affirmed the models robustness. O_TBL View this table: org.highwire.dtl.DTLVardef@1df407eorg.highwire.dtl.DTLVardef@3436borg.highwire.dtl.DTLVardef@3f51eaorg.highwire.dtl.DTLVardef@11b1338org.highwire.dtl.DTLVardef@8ae914_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSummary of Causal Effects Across Model Conditions Average treatment effects (ATEs), confidence intervals, and p-values are shown for key model paths. TOST testing assessed equivalence of Purkinje cell impact using {+/-}0.015 margin. Interaction and robustness outcomes are reported descriptively. C_TABLECAPTION C_TBL Reproducibility and Perturbation TestingFor reproducibility evaluation, the synthetic pipeline was re-run under modified scenarios: (1) DAG perturbation by removing the Thalamus [->] GABAergic Tone edge to examine relay dependency, and (2) parameter shifts by adjusting GABA coefficient priors by {+/-}10% to emulate biological variability. Each perturbation generated a fresh synthetic cohort (n = 10,000), with recomputation of ATEs, mediation estimates, and ANOVA terms. Comparisons to the baseline run confirmed stability in effect directions and significance thresholds. InterpretationThis multivariable modeling approach implies that cerebellar stimulation may mitigate modeled seizure burden predominantly via timely application rather than reliance on baseline Purkinje cell integrity. Recent empirical studies reinforce cerebellar structural alterations in TLE and the potential of non-invasive stimulation techniques, such as repetitive transcranial magnetic stimulation (rTMS), to induce vermis volume changes correlated with seizure reduction (So et al., 2024). Additionally, ongoing clinical trials exploring transcranial alternating current stimulation targeting the cerebellum in refractory TLE align with our timing-sensitive findings. All results stem from biologically informed synthetic cohorts and are positioned to inform empirical validation in translational contexts. ConclusionModel-derived insights highlight the optimization of cerebellar stimulation timing as a promising, testable avenue for modulating hippocampal excitability in TLE, irrespective of underlying Purkinje cell status. These findings underscore the value of synthetic frameworks in hypothesizing dynamic intervention strategies.

neuroscience↗

bioRxiv2025

Investigating the relationship Between AMBRA1 and Cell Proliferation in Melanoma

The protein Activating molecule in Beclin1-regulated autophagy1 (AMBRA1), discovered in 2007, is crucial for autophagy and plays roles in nervous system development, cell survival, and proliferation. This study investigates AMBRA1s involvement in various cellular processes using a systems-based "omics" approach, focusing on melanoma. Transcriptomic analysis of the overexpression or the knock-down of AMBRA1 was shown to result in significant dysregulation of several transcripts. This appears to have identified several novel roles for AMBRA1 in a range of cellular pathways; some of these are hallmarks of cancer signaling including, MAPK, angiogenesis, tissue growth factor signaling, axon guidance and Wnt signaling. Yeast two-hybrid assays performed in this study identified novel binding partners that can provide evidence for new roles for AMBRA1 in different cellular processes. The work shows that AMBRA1 loss appears to upregulate metastatic genes/proteins supporting the role of AMBRA1 as a tumor suppressor gene in melanoma.

cancer biology↗

bioRxiv2025

Lack of consistent effect of dietary fiber on immune checkpoint blockade efficacy across diverse murine tumor models

Immune checkpoint blockade (ICB) has transformed cancer treatment, but success rates remain low in most cancers. Recent research suggest that dietary fiber enhances ICB response in melanoma patients and murine preclinical models through microbiome-dependent mechanisms. Yet, the robustness of this effect across cancer types and dietary contexts remains unclear. Specifically, prior literature compared grain-based chow (high fiber) to low-fiber purified diet, but these diets differ also on other dimensions including phytochemicals. Here we investigated, in mice fed grain-based chow or purified diets with differing quantities of isolated fibers (cellulose and inulin), metabolite levels and ICB activity in multiple tumor models. The blood and fecal metabolome were relatively similar between mice fed high- and low-fiber purified diets, but differed massively between mice fed purified diets or chow, identifying the factor as diet type, independent of fiber. Tumor growth studies in three implantable and two spontaneous genetically engineered tumor models revealed that fiber has a weaker impact on ICB (anti-PD-1) efficacy than previously reported. In some models, dietary modulation impacted ICB activity, but not in a consistent direction across models. In none of the models did we observe the pattern expected if fiber controlled ICB efficacy: strong efficacy in both chow and high-fiber purified diet but low efficacy in low-fiber purified diet. Thus, dietary fiber appears to have limited or inconsistent effect on ICB efficacy in mouse models, and other dietary factors that correlate with fiber intake may underlie the clinical correlations between fiber consumption and immunotherapy outcomes.

cancer biology↗