Biology subjects

Diamante, G.

Publications and source records attributed to Diamante, G..

12 recordsLinked to original sources

bioRxiv2026

Genotype-phenotype mapping identifies fetal-like CD55+ immunoregulatory cancer cells as mediators of immune escape in colorectal cancer

Immune evasion is a defining feature of advanced colorectal cancer (CRC), yet the cellular mechanisms linking cancer cell states to immune suppression remain poorly understood. To systematically map tumour-immune interactions in advanced CRC, we modelled recurrent human CRC mutations using a multiplex CRISPR-based genetically engineered mouse model platform. The resulting 20 models recapitulate key stages, genetic routes and histopathological features of human CRC, while single-cell transcriptomics reveals extensive disease complexity across models. Profiling of the epithelial tumour compartment identified a population of fetal-like immunoregulatory cancer cells (IRCs) characterized by interferon-{gamma} and MAPK activity. IRCs are marked by expression of the membrane-bound complement regulatory protein CD55. Mechanistically, CD55 protects IRCs from immune surveillance and complement-mediated lysis. Together, these findings reveal a cancer cell-immune interface that promotes immune evasion in advanced CRC.

cancer biology↗

bioRxiv2026

WNT-driven immune evasion promotes malignant transformation of BRAF-mutant colorectal cancer

BRAF-mutant colorectal cancer (CRC) constitutes a molecularly and clinically distinct subtype with poor prognosis and resistance to standard therapies, representing a major unmet clinical need. Arising from the serrated pathway of colorectal carcinogenesis rather than the classical adenoma-carcinoma sequence, this subgroup remains relatively understudied yet displays a more aggressive disease course. To investigate the progression of serrated CRC, we generated multiple genetically engineered mouse models (GEMMs) of BRAF-mutant, microsatellite-stable (MSS) CRC that closely recapitulate human disease. Our findings demonstrate that WNT-pathway activation via APC- or CTNNB1-mutations, but not RNF43-loss, initiates serrated CRC by suppressing immune-mediated tumor surveillance. Mechanistically, WNT-signaling drives distinct alterations in T cell phenotypes within the tumor microenvironment, enabling tumor progression. Together, these data indicate that WNT-signaling mediates immune escape during the malignant transformation of BRAF-mutant CRC.

cancer biology↗

bioRxiv2025

Relative contribution of gonads and sex chromosomes to sex differences in cell-type gene expression in the mouse medial septum and sex-biased disease risk

BackgroundWhile sex differences in the brain have traditionally been attributed to gonadal hormones, emerging evidence points to regulation by sex chromosomes. This study aims to differentiate the influence of gonads versus sex chromosomes on cellular gene expression in the mouse medial septum (MS), a critically understudied brain region. MethodsUsing single nucleus RNA-sequencing and the Sex Chromosome Trisomy mouse model, we (1) quantified sex differences in cellular gene expression and (2) isolated sex-biasing effects by identifying perturbed cell types, differentially expressed genes, biological pathways, and gene networks, which were integrated with GWAS data to explore links with sex-biased human phenotypes. ResultsOur analysis revealed that volumetric sex differences in the MS are mirrored by widespread transcriptomic changes across cell types. Critically, genetic effects displayed elevated relevance compared to sex hormones in driving sex-biased gene expression. These effects converge to regulate synaptic/neuronal development, transcriptional regulation, and cellular metabolism. Sex chromosome-associated DEGs were enriched for various human disorders, suggesting a cellular and mechanistic basis for their sex-biased patterns. ConclusionsOur findings challenge the classical gonad-centric views of sexual differentiation, as the MS displays sex-biased transcriptional regulation driven by sex chromosome-associated effects that are highly relevant for human health.

neuroscience↗

bioRxiv2025

Trimethylamine-N-oxide affects cell type-specific pathways and networks in mouse aorta to promote atherosclerotic plaque vulnerability

BackgroundTrimethylamine-N-oxide (TMAO) has been significantly linked to atherosclerosis via several mechanisms, but its direct effect on the atherosclerosis-prone vasculature remains unclear. The objective of this study was to characterize the cell type-dependent and independent effects of TMAO on key vascular cell types involved in atherosclerosis progression in vivo. MethodsWe performed single cell RNA-sequencing (scRNAseq) on aortic athero-prone regions of female Ldlr-/- mice fed control Chow, high-cholesterol (HC), or HC+TMAO diets for three months to identify which aortic cell types, differentially expressed genes, and biological pathways are affected by TMAO. We also modeled cell-cell communications and intracellular gene regulatory networks to identify gene networks perturbed by TMAO feeding. Key genes and pathways were validated using primary human smooth muscle cells exposed to TMAO. Changes in the thickness of lesional fibrous caps in response to TMAO in female Ldlr-/- mice fed HC+TMAO versus HC diets were measured using transgelin immunostaining. ResultsOur scRNAseq analysis revealed that TMAO supplementation upregulated apoptotic gene signatures and downregulated extracellular matrix (ECM) organization and collagen formation genes in a subset of atherosclerosis-specific modulated vascular smooth muscle cells (vSMCs). We also identified "degradation of the ECM" as a top pathway for SMC-derived macrophage DEGs in response to TMAO. Network analyses support that macrophage-vSMC communication mediates ECM remodeling. Using human smooth muscle cells exposed to TMAO in vitro, we confirmed the direct effect of TMAO on regulating collagen and apoptotic genes. In agreement with the changes in these pathways that affect plaque stability, we observed a significant decrease in fibrous cap thickness in mice supplemented with TMAO. ConclusionsOur results reveal the effects of TMAO on vSMCs to promote apoptosis and decrease ECM formation, and on macrophage-mediated ECM degradation in atherosclerotic lesions to in concert enhance plaque instability. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/640205v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@100254org.highwire.dtl.DTLVardef@109155aorg.highwire.dtl.DTLVardef@158d280org.highwire.dtl.DTLVardef@63d544_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIscRNAseq of the aortic athero-prone regions in female Ldlr-/- mice supplemented with TMAO in the diet revealed the effect of TMAO across cell types, particularly in SMC-derived macrophages and atheroprotective modulated vSMCs. C_LIO_LITMAO increases apoptotic gene signatures and reduces ECM organization and collagen formation gene signatures in modulated vSMCs in vivo, and in vitro exposure studies support a direct effect of TMAO on these genes. C_LIO_LIModulated vSMC-specific gene regulatory networks enriched for apoptotic genes and ECM organization genes were organized by intracellular regulators such as Ccl19 and Tnn and extracellular regulators such as Mmp9 and Spp1 from macrophages. C_LIO_LIFibrous cap thickness, a marker of atherosclerotic plaque stability, was significantly reduced in female Ldlr-/- mice fed HC+TMAO versus HC diets for five months. C_LI

physiology↗

bioRxiv2025

Glo1 reduction in mice results in age- and sex-dependent metabolic dysfunction

ObjectivesAdvanced glycation end products (AGEs) have been implicated as an important mediator of metabolic disorders including obesity, insulin resistance, and coronary artery disease. Glyoxalase 1 (Glo1) is a critical enzyme in the clearance of toxic dicarbonyl such as methylglyoxal, precursors of AGEs. The role of AGE-independent mechanisms that underly Glo1-induced metabolic disorders have yet to be elucidated. MethodsWe performed a longitudinal study of female and male Glo1 heterozygous knockdown (Glo1+/-) mice with [~]50% gene expression and screened metabolic phenotypes such as body weight, adiposity, glycemic control and plasma lipids. We also evaluated atherosclerotic burden, AGE levels, and gene expression profiles across cardiometabolic tissues (liver, adipose, muscle, kidney and aorta) to identify pathway perturbations and potential regulatory genes of Glo1 actions. ResultsPartial loss of Glo1 resulted in obesity, hyperglycemia, dyslipidemia, and alterations in lipid metabolism in metabolic tissues in an age- and sex-dependent manner. Glo1+/- females displayed altered glycemic control and increased plasma triglycerides, which aligned with significant perturbations in genes involved in adipogenesis, PPARg, insulin signaling, and fatty acid metabolism pathways in liver and adipose tissues. Conversely, Glo1+/- males developed increased skeletal muscle mass and visceral adipose depots along with changes in lipid metabolism pathways. For both cohorts, most phenotypes manifested after 14 weeks of age. Evaluation of methylglyoxal-derived AGEs demonstrated changes in only male skeletal muscle but not in female tissues, which cannot explain the broad metabolic changes observed in Glo1+/-mice. Transcriptional profiles suggest that altered glucose and lipid metabolism may be partially explained by alternative detoxification of methylglyoxal to metabolites such as pyruvate. Moreover, transcription factor (TF) analysis of the tissue-specific gene expression data identified TFs involved in cardiometabolic diseases such as Hnf4a (all tissues) and Arntl (aorta, liver, and kidney) which are female-biased regulators and whose targets are altered in response to Glo1+/-. ConclusionsOur results indicate that Glo1 reduction perturbs metabolic health and metabolic pathways in a sex- and age-dependent manner without significant changes in AGEs across metabolic tissues. Rather, tissue-specific gene expression analysis suggests that key transcription factors such as Hfn4a and Arntl as well as metabolite changes from alternative methylglyoxal detoxification such as pyruvate, likely contribute to metabolic dysregulation in Glo1+/- mice.

molecular biology↗

bioRxiv2023

Prdm16 and Vcam1 regulate the postnatal disappearance of embryonic radial glia and the ending of cortical neurogenesis

Embryonic neural stem cells (NSCs, i.e., radial glia) in the ventricular-subventricular zone (V-SVZ) generate the majority of neurons and glia in the forebrain. Postnatally, embryonic radial glia disappear and a subpopulation of radial glia transition into adult NSCs. As this transition occurs, widespread neurogenesis in brain regions such as the cerebral cortex ends. The mechanisms that regulate the postnatal disappearance of radial glia and the ending of embryonic neurogenesis remain poorly understood. Here, we show that PR domain-containing 16 (Prdm16) promotes the disappearance of radial glia and the ending of neurogenesis in the cerebral cortex. Genetic deletion of Prdm16 from NSCs leads to the persistence of radial glia in the adult V-SVZ and prolonged postnatal cortical neurogenesis. Mechanistically, Prdm16 induces the postnatal reduction in Vascular Cell Adhesion Molecule 1 (Vcam1). The postnatal disappearance of radial glia and the ending of cortical neurogenesis occur normally in Prdm16-Vcam1 double conditional knockout mice. These observations reveal novel molecular regulators of the postnatal disappearance of radial glia and the ending of embryonic neurogenesis, filling a key knowledge gap in NSC biology.

neuroscience↗

bioRxiv2022

Thyroid Hormone T4 Mitigates Traumatic Brain Injury via Dynamically Remodeling Cell Type Specific Genes and Pathways

BackgroundThe complex pathology of mild traumatic brain injury (mTBI) is a main contributor to the difficulties in achieving a successful therapeutic regimen. Thyroxine (T4) administration has been shown to prevent the cognitive impairments induced by mTBI in mice. MethodTo understand the underlying mechanism, we carried out a single cell transcriptomic study to investigate the spatiotemporal effects of T4 on individual cell types in the hippocampus and frontal cortex at three post-injury stages. FindingsOur multi-tissue multi-stage results showed that T4 treatment altered the proportions and transcriptomes of numerous cell types across tissues and timepoints, particularly oligodendrocytes, astrocytes, and microglia, which are crucial for injury repair. T4 also reversed the expression mTBI-affected genes such as Ttr, mt-Rnr2, Ggn12, Malat1, Gnaq, and Myo3a, as well as numerous pathways such as cell/energy/iron metabolism, immune response, nervous system, and cytoskeleton-related pathways. Cell-type specific network modeling revealed that T4 mitigated select mTBI-perturbed dynamic shifts in subnetworks related to cell cycle, stress response, and RNA processing in oligodendrocytes. Cross cell-type ligand-receptor networks recapitulated the roles of App, Hmgb1, Fn1, and Tnf in mTBI, the latter two ligands having been previously identified as TBI network hubs. mTBI and/or T4 signature genes were enriched for human genome-wide association study (GWAS) candidate genes for cognitive, psychiatric and neurodegenerative disorders related to mTBI, supporting T4 as a potential mTBI treatment. InterpretationOur systems-level approach elucidated the temporal and spatial dynamic reprogramming of cell-type specific genes, pathways, and networks, as well as cell-cell communications through which T4 mitigates cognitive dysfunction induced by mTBI. FundingThis work was funded by NIHR01NS117148 to X.Y. and F.G.P. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSDysfunction in the brain resulting from traumatic brain injury can display immediately as well as several years post-injury. It also impacts various brain regions, including the hippocampus and frontal cortex, which are linked to distinct disease pathologies. The complexity of spatiotemporal and molecular dynamics of perturbation caused by TBI hinder our ability to establish an effective therapeutic approach. Recently, thyroid hormone poses promise as a potential therapeutic target based on our previous scRNA-seq studies. Yet, the mechanisms by which T4 alleviates mTBI, specifically those related to spatial, temporal, and cell-type specificity, remain unexplored. Added value of this studyWe examined the impact of T4 intervention in mitigating mTBI by investigating the transcriptome and functional pathways across two affected brain regions, the frontal cortex and hippocampus, in different stages of injury. Utilizing a systems biology approach, we conducted within- and between-cell-type network modeling, cell-cell communication and integrating human genome-wide association studies (GWAS) analysis. This comprehensive strategy aimed to elucidate the cellular and molecular mechanisms through which T4 averts cognitive impairments induced by mTBI. Implications of all the available evidenceOur findings offer molecular evidence that the administration of T4 impacts a wide range of genes, biological processes, and networks, thereby preventing the advancement of mTBI-induced brain dysfunction and associated diseases. This comprehensive impact of T4 suggests potential advantages in efficacy compared to other therapeutic options that concentrate on specific pathways and targets.

neuroscience↗

bioRxiv2022

Cross-tissue multiomics studies reveal gut-brain interactions mediating the effect of Akkermansia muciniphila in counteracting fructose-induced obesity

High fructose diet is a major risk factor for metabolic syndrome (MetS). The gut bacterium Akkermansia muciniphila (A. muciniphila) has been shown to improve fructose-induced MetS, but the underlying mechanism remains unclear. Here, we investigated how A. muciniphila modulates fructose-induced MetS using multitissue, multiomics studies encompassing gut microbiota, plasma and gut metabolome, and hypothalamus single cell RNA-sequencing. A. muciniphila colonization enriched beneficial gut bacteria, increased metabolites including bile acids, endocannabinoids, and vitamins, and activated genes related to oxytocin and vasopressin signaling in hypothalamic neurons. Multiomics network analysis prioritized the metabolite oleoylethanolamide (OEA), an endocannabinoid analogue, as a potential regulator of gut-hypothalamic interaction conferred by A. muciniphila, its associated beneficial bacteria, and bile acid remodeling. Oral administration of OEA to fructose-fed mice recapitulated A. muciniphila effects, including counteracting body weight gain, enhancing thermogenesis, and ameliorating glucose intolerance. Concomitantly, OEA supplementation stimulated expression of its receptors and tight junction genes in the intestine, as well as neuronal activation marker c-Fos and oxytocin and vasopressin signaling genes in the hypothalamus. These findings underscore the regulatory role of A. muciniphila in gut microbiota homeostasis and metabolomic reprogramming, and pinpoint OEA as a key mediator of its action on the gut-hypothalamus axis in alleviating fructose-induced MetS.

systems biology↗

bioRxiv2020

Cold-associated mammokines preserve adipocyte identity

Sympathetic activation during cold exposure increases adipocyte thermogenesis via expression of mitochondrial protein uncoupling protein 1 (UCP1)1. The propensity of adipocytes to express UCP1 is under a critical influence of the adipose microenvironment and varies among various fat depots2-7. Here we report that cold-induced adipocyte UCP1 expression in female mouse subcutaneous white adipose tissue (scWAT) is regulated by mammary gland ductal epithelial cells in the adipose niche. Single cell RNA-sequencing (scRNA-seq) show that under cold condition glandular alveolar and hormone-sensing luminal epithelium subtypes express transcripts that encode secretory factors involved in regulating adipocyte UCP1 expression. We term mammary duct secretory factors as "mammokines". Using whole-tissue immunofluorescence 3D visualization, we reveal previously undescribed sympathetic nerve-ductal points of contact and show that sympathetic nerve-activated mammary ducts limit adipocyte UCP1 expression via cold-induced mammokine production. Both in vivo and ex vivo ablation of mammary ductal epithelium enhances cold-induced scWAT adipocyte thermogenic gene program. The mammary duct network extends throughout most scWATs in female mice, which under cold exposure show markedly less UCP1 expression, fat oxidation, energy expenditure, and subcutaneous fat mass loss compared to male mice. These results show a previously uncharacterized role of sympathetic nerve-activated glandular epithelium in adipocyte thermogenesis. Overall, our findings suggest an evolutionary role of mammary duct luminal cells in defending glandular adiposity during cold exposure, highlight mammary gland epithelium as a highly active metabolic cell type, and implicate a broader role of mammokines in mammary gland physiology and systemic metabolism.

cell biology↗

bioRxiv2020

Hypothalamic estrogen receptor alpha mediates key side effects of tamoxifen therapy in mice

Adjuvant tamoxifen therapy for invasive breast cancer improves patient survival. Unfortunately, long-term treatment comes with side effects that impact health and quality of life, including hot flashes, changes in bone density, and fatigue. Partly due to a lack of proven animal models, the tissues and cell types that mediate these negative side effects are largely unknown. Here we show that mice undergoing a 28-day course of tamoxifen treatment experience dysregulation of core and skin temperature, changes in bone density, and decreased physical activity, recapitulating key aspects of the human physiological response. Single cell RNA sequencing reveals that tamoxifen treatment induces significant and widespread gene expression changes in different cell types of the hypothalamus, most strongly in neurons and ependymal cells. These expression changes are dependent on estrogen receptor alpha (ER), as conditional knockout of ER in the hypothalamus ablated or reversed tamoxifen-induced gene expression. Accordingly, ER-deficient mice do not exhibit changes in thermal regulation, bone density, or movement in response to tamoxifen treatment. These findings provide mechanistic insight into the effects of tamoxifen on the hypothalamus and support a model in which hypothalamic ER mediates several key side effects of tamoxifen therapy.

neuroscience↗

bioRxiv2019

PharmOmics: A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing

Drug development has been hampered by a high failure rate in clinical trials due to efficacy or safety issues not predicted by preclinical studies in model systems. A key contributor is our incomplete understanding of drug functions across organ systems and species. Therefore, elucidating species- and tissue-specific actions of drugs can provide systems level insights into therapeutic efficacy, potential adverse effects, and interspecies differences that are necessary for more effective translational medicine. Here, we present a comprehensive drug knowledgebase and analytical tool, PharmOmics, comprised of genomic footprints of drugs in individual tissues from human, mouse, and rat transcriptome data from GEO, ArrayExpress, TG-GATEs, and DrugMatrix. Using multi-species and multi-tissue gene expression signatures as molecular indicators of drug functions, we developed gene network-based approaches for drug repositioning. We demonstrate the potential of PharmOmics to predict drugs for new disease indications and validated two predicted drugs for non-alcoholic fatty liver disease in mice. We also examined the potential of PharmOmics to identify drugs related to hepatoxicity and nephrotoxicity. By combining tissue- and species-specific in vivo drug signatures with biological networks, PharmOmics serves as a complementary tool to support drug characterization.

systems biology↗

bioRxiv2019

Single Cell Analysis Reveals Immune Cell-Adipocyte Crosstalk Regulating the Transcription of Thermogenic Adipocytes

Immune cells are vital constituents of the adipose microenvironment that influence both local and systemic lipid metabolism. Mice lacking IL10 have enhanced thermogenesis, but the roles of specific cell types in the metabolic response to IL10 remain to be defined. We demonstrate here that selective loss of IL10 receptor in adipocytes recapitulates the beneficial effects of global IL10 deletion, and that local crosstalk between IL10-producing immune cells and adipocytes is a determinant of thermogenesis and systemic energy balance. Single Nuclei Adipocyte RNA-sequencing (SNAP-seq) of subcutaneous adipose tissue defined a metabolically-active mature adipocyte subtype characterized by robust expression of genes involved in thermogenesis whose transcriptome was selectively responsive to IL10R deletion. Furthermore, single-cell transcriptomic analysis of adipose stromal populations identified lymphocytes as a key source of IL10 production in response to thermogenic stimuli. These findings implicate adaptive immune cell-adipocyte communication in the maintenance of adipose subtype identity and function.

cell biology↗