Biology subjects

Golani, O.

Publications and source records attributed to Golani, O..

15 recordsLinked to original sources

bioRxiv2026

Persistent stromal reprogramming defines incomplete mucosal healing and predicts therapeutic response in ulcerative colitis

Mucosal healing (MH) is the primary therapeutic endpoint in ulcerative colitis (UC), yet frequent relapses suggest it does not reflect complete tissue recovery. To define the basis of this vulnerability, we generated a multimodal atlas of UC integrating single-cell and bulk transcriptomics, Visium HD spatial profiling, and multiplexed imaging across 89 patients. We show that MH represents a distinct biological state marked by persistent stromal remodeling along three axes: emergence of inflammatory fibroblasts, sustained loss of OGN niche-supporting fibroblasts, and expansion of pericytes with matrix-remodeling features and reduced vascular association. Spatial analyses revealed persistent reorganization of mucosal tissue domains despite apparent clinical remission. Across independent cohorts, baseline inflammatory fibroblast and pericyte signatures robustly predicted non-response to anti-TNF therapy. These findings suggest that patients in MH remain in a biologically altered state linked to relapse risk and identify stromal reprogramming as a determinant of disease persistence and therapeutic response in UC.

immunology↗

bioRxiv2026

A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid

Many organs are organized into repeating anatomical units, yet how cellular heterogeneity is structured within and between these units remains poorly understood. Here we use spatial transcriptomics to dissect multiscale heterogeneity in the human thyroid gland, a tissue composed of hormone-producing follicles. Across human thyroid samples spanning non-inflamed to inflamed states, we develop a follicle-aware analytical framework that separates intra-follicular from inter-follicular variability. We find that heterogeneity among thyrocytes is not dominated by differences in hormone synthesis but instead by two opposing transcriptional programs: an active hormone-producing state and a damage-response thyrocyte (DRT) state enriched for stress, immune, and damage-response pathways. DRTs are spatially clustered, associated with DNA damage markers, and are enriched near immune niches. Notably, the balance between active and damage-response programs constitutes a major axis of variability across cells, follicles, and patients. Our findings highlight a damage-response epithelial thyrocyte state that may be fundamental to follicular function in the human thyroid and provide a general framework for studying heterogeneity in tissues composed of repeating anatomical units.

systems biology↗

bioRxiv2026

Spatial analysis reveals the evolving organization of low-grade and high-grade IDH-mutant glioma

Adult diffuse gliomas are comprised of malignant cell states interwoven with the non-malignant brain microenvironment. Here we combine spatial transcriptomics and spatial proteomics of IDH-mutant gliomas to define organizational principles across histological grades. In low-grade tumors, spatial organization arises from underlying nonmalignant brain structures. For example, we classify low-grade tumor regions as embedded into white matter and identify a sharp white-grey matter junction that restricts cortical invasion and is associated with marked changes in tumor composition and cellular phenotypes. This junction is preferentially traversed by oligodendrocyte progenitor (OPC)-like malignant cells, which may drive tumor expansion. In contrast, intermediate-grade tumors are largely disorganized, with few recurring pairwise interactions between cancer cell states and TME cell types. In high-grade tumors, hypoxia/necrosis-associated global structure begins to emerge, reminiscent of IDH-wildtype glioblastoma. Together, these findings reveal two independent axes of glioma spatial organization--from brain anatomy-driven organization in low-grade tumors to hypoxia-associated structure in high-grade tumors--and establishes a framework that links tumor grade to recurrent spatial associations between cell states and cell types.

cancer biology↗

bioRxiv2026

Spatial Rewiring of Enterocyte Identity in Celiac Disease

Enterocytes in the human small intestine exhibit distinct functional states in different zones along the crypt-villus axis, a feature that is thought to convey optimal absorption. In celiac disease (CeD), autoimmune destruction of enterocytes leads to villus blunting, but how this altered tissue morphology affects enterocyte states is unclear. Using spatial and single-cell transcriptomics, we show that in patients with CeD, enterocytes acquire a novel identity characterized by co-expression of multiple zonal programs. This aberrant zonal co-expression results from reduced distances between BMP- and WNT-producing mesenchymal cells, leading to overlapping morphogen fields. In addition, we identify a subset of metaplastic cells that adopt gastric pit cell-like identities in discrete tissue patches. Our findings provide a detailed view of epithelial remodeling in CeD and establish a resource for understanding the cellular basis of malabsorption associated with villus blunting.

systems biology↗

bioRxiv2025

Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics

Subcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics (VisiumHD) to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that extracts subcellular features from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures that can be readily obtained from standard high-definition spatial transcriptomics experiments. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.

systems biology↗

bioRxiv2025

A pharmacological modality to sequester homomeric proteins

Molecules that can perturb protein-protein interactions have an immense impact on chemical biology and therapeutics. However, such compounds typically rely on accessory proteins to function, such as E3 ligases in the case of targeted degradation, which may restrict their target and tissue scope or lead to resistance. Here we alleviate the need for accessory proteins with a novel pharmacological modality to knock-down protein function. Our strategy exploits protein symmetry as a selective vulnerability, and is widely applicable owing to the ubiquitous nature of homomeric proteins in cellular systems. We target homomeric proteins with PINCHs (Polymerization Inducing Chimeras) - bifunctional molecules composed of two linked ligands that act as bridges between homomers and trigger their supramolecular assembly into insoluble polymers. We design PINCHs that achieve efficient polymerization of three homomeric targets. In cells, we observed that a PINCH targeting Keap1 exhibited a longer duration of action compared to its monomeric inhibitor, and a PINCH targeting BCL6 displayed selective and improved B cell toxicity compared to its monomeric parent. Our results highlight PINCHs as a novel and general strategy to modulate and knock out protein function.

biochemistry↗

bioRxiv2025

A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver

Reconstructing gene expression atlases for human tissues is challenging due to limited access to healthy samples from live donors. Neurologically deceased donors often show ischemic changes, while tissues near diseased regions may have altered gene expression. The liver, with its unique regenerative capacity, allows analysis from live healthy donors (LHDs). Using spatial transcriptomics (Visum, Visium HD and MERFISH), we analyzed 16 liver samples: eight from young LHDs and eight from patients with liver pathology, sampling adjacent normal tissue. LHD livers displayed significant gene expression differences from adjacent normal tissues. Hepatocytes exhibited marked zonation along the porto-central axis of liver lobules, with key functions pericentrally shifted compared to other mammals. Our atlas identified dynamic programs in early steatotic hepatocytes, showing transitions from lipid uptake in low-lipid regions to insulin hypersensitivity in high-lipid regions. This study presents a spatial gene expression reference for the healthy human liver and insights into hepatocyte adaptations in steatosis.

cell biology↗

bioRxiv2023

Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion

Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, even highly homogenous tumors may display variability in their aggressiveness, and how immunologic-factors impinge on their aggressiveness remains understudied. Here we studied the mechanisms responsible for the immune-escape of murine tumors with low ITH. We compared the temporal growth of homogeneous, genetically-similar single-cell clones that are rejected vs. those that are not- rejected after transplantation in-vivo using single-cell RNA sequencing and immunophenotyping. Non- rejected clones showed high infiltration of tumor-associated-macrophages (TAMs), lower T-cell infiltration, and increased T-cell exhaustion compared to rejected clones. Comparative analysis of rejection- associated gene expression programs, combined with in-vivo CRISPR knockout screens of candidate mediators, identified Mif (macrophage migration inhibitory factor) as a regulator of immune rejection. Mif knockout led to smaller tumors and reversed non-rejection-associated immune composition, particularly, leading to the reduction of immunosuppressive macrophage infiltration. Finally, we validated these results in melanoma patient data. Statement of significanceHere, we uncover the association of Mif expression with tumor growth and aggressiveness, specifically in low ITH tumors. These findings could facilitate the development of new strategies to treat patients with homogeneous, high-MIF expressing tumors that are unresponsive to immune checkpoint therapy.

cancer biology↗

bioRxiv2023

Egg MVBs elicit an antimicrobial pathway to degrade paternal mitochondria after fertilization

Mitochondria are maternally inherited, but the mechanisms underlying paternal mitochondrial elimination (PME) after fertilization are far less clear. Using Drosophila, we show that special egg-derived multivesicular bodies (MVBs) promote PME by activating LC3-associated phagocytosis (LAP), a cellular defense pathway commonly employed against invading microbes. Upon fertilization, the egg MVBs engage and densely coat the sperm flagellum, forming extended flagellum vesicular sheaths (FVSs), within which the paternal mitochondria degrade. Inactivation of multiple LAP pathway components, such as Rubicon, a LAP-specific class III PI(3)K complex protein, significantly attenuates PME. Furthermore, recruitment of Atg8/LC3 to the FVS requires both Rubicon and the Atg8/LC3 conjugation machinery. Other LAP pathway events, such as production of the phospholipid PtdIns(3)P and reactive oxygen species (ROS), also unfold during PME. Finally, we provide evidence that a similar pathway might also mediate PME in mammals, highlighting the notion that eggs may regard paternal mitochondria as potentially dangerous trespassers.

developmental biology↗

bioRxiv2023

Metabolic rewiring of the probiotic bacterium Lacticaseibacillus rhamnosus GG contributes to cell wall remodeling and antimicrobials production

Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under conditions of oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture in LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced secretion of known and novel metabolites and proteins targeting the enteric pathogens Enterococcus faecalis and Salmonella Enterica serovar Typhimurium. Overall, our results link the common metabolic regulation of cell wall remodeling, aggregation to host tissues, biofilm formation in probiotic strains, and connect the production of antimicrobial effectors with metabolome reprogramming. These findings provide novel insights into the role of nutrition in the establishment of LGG in the gastrointestinal tract.

microbiology↗

bioRxiv2022

The differential regulation of placenta trophoblast bisphosphoglycerate mutase in fetal growth restriction: preclinical study in mice and observational histological study of human placenta.

BackgroundFetal growth restriction (FGR) is a pregnancy complication in which a newborn fails to achieve its growth potential, increasing the risk of perinatal morbidity and mortality. Chronic maternal gestational hypoxia, as well as placental insufficiency are associated with increased FGR incidence; however, the molecular mechanisms underlying FGR remain unknown. MethodsIn a case control study of murine and human control and FGR placentae, we implied MR imaging, IHC and metabolomics to assess the levels of BPGM and 2,3 BPG to elucidate the impact of maternal gestational hypoxia, and the molecular mechanisms underlying human FGR. ResultsWe show that murine acute and chronic gestational hypoxia recapitulates FGR phenotype and affects placental structure and morphology. Gestational hypoxia decreased labyrinth area, increased the incidence of red blood cells (RBCs) in the labyrinth while expanding the placental spiral arteries (SpA) diameter. Hypoxic placentae exhibited higher hemoglobin-oxygen affinity compared to the control. Placental abundance of bisphosphoglycerate mutase (BPGM) was upregulated in the syncytiotrophoblast and spiral artery trophoblast cells (SpA TGCs) in the murine gestational hypoxia groups compared to the control. In contrast, human FGR placentae exhibited reduced BPGM levels in the syncytiotrophoblast layer compared to placentae from healthy uncomplicated pregnancies. Levels of 2,3 BPG, the product of BPGM, were lower in cord serum of human FGR placentae compared to control. Polar expression of BPGM, was found in both human and mouse placentae syncytiotrophoblast, with higher expression facing the maternal circulation. Moreover, in the murine SpA TGCs expression of BPGM was concentrated exclusively in the apical cell side, in direct proximity to the maternal circulation. ConclusionsThis study suggests a possible involvement of placental BPGM in maternal-fetal oxygen transfer, and in the pathophysiology of FGR. FundingThis work was supported by the Weizmann - Ichilov (Tel Aviv Sourasky Medical Center) Collaborative Grant in Biomedical Research (to MN) and by the Israel Science Foundation KillCorona grant 3777/19 (to MN, MK). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC="FIGDIR/small/507932v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@500160org.highwire.dtl.DTLVardef@8a68a9org.highwire.dtl.DTLVardef@dd60c3org.highwire.dtl.DTLVardef@1fbb209_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2022

De-tensioning of collagen fibers optimizes endometrial receptivity and improves the rate of embryo implantation

Successful embryo implantation within the uterine wall requires intricate endometrial remodeling. Impaired endometrial receptivity, a common cause of infertility, often results from ineffective remodeling processes. Here, we demonstrate that a single dose of human collagenase-1 administered into the mouse uterus enhances embryo implantation rates. Mechanistically, collagenase-1 induces remodeling of the endometrial extracellular matrix (ECM), leading to the degradation of collagen fibers and proteoglycans. This process releases matrix-bound bioactive factors, such as VEGF, which facilitates local vascular permeability and angiogenesis. Furthermore, collagenase-1 treatment increases NK cell infiltration and elevates levels of the cytokine LIF, a key factor in embryo implantation. Remarkably, the overall structural integrity of the uterine tissue remains uncompromised, even in the presence of reduced tension in endometrial collagen fibers. To assess pre-clinical potential, in-uteri application of collagenase-1 successfully rescued implantation in mouse models subjected to heat stress and embryo transfer, conditions known for their adverse impact on implantation rates. Importantly, ex-vivo exposure of human uterine tissue to collagenase-1 induced collagen de-tensioning and the release of VEGF, demonstrating similar processes observed in the mouse settings, and the potential relevance of this treatment to human conditions. Our findings underscore the immense clinical potential and feasibility of collagenase treatment to enhance uterine receptivity for embryo implantation, offering a controlled and minimally invasive intervention. This innovative approach not only demonstrates the potential to enhance efficiency in livestock breeding but, more importantly, signifies a substantial promise in supporting medical interventions for human reproduction in clinical settings.

biochemistry↗

bioRxiv2020

Hyaluronan-NK cell Interaction Controls the Primary Vascular Barrier during Early Pregnancy

Successful implantation is associated with a unique spatial pattern of vascular remodeling, characterized by profound peripheral neo-vascularization surrounding a peri-embryo avascular niche. We hypothesized that hyaluronan controls the formation of the unique vascular pattern encompassing the embryo. This hypothesis was evaluated by genetic modification of hyaluronan metabolism specifically targeted to embryonic trophoblast cells. The outcome of altered hyaluronan deposition on uterine vascular remodeling and post-implantation development were analyzed by MRI, detailed histological examinations, and RNA-sequencing of uterine NK cells. Our experiments revealed that eliminating the anti-angiogenic hyaluronan, led to elevated expression of MMP-9, VEGF-A and its receptor VEGFR-2, accompanied by reduced recruitment of uterine NK cells. Further local decrease in VEGFR-3 resulted in impaired formation of vascular sinuous folds, ectopic angiogenesis and dysfunctional uterine NK cells. Conversely, enhanced deposition of hyaluronan caused the expansion of the maternal-embryo barrier, leading to an increased diffusion distance and aborted implantation. These results demonstrate a pivotal role for hyaluronan in successful pregnancy by fine-tuning the peri-embryo avascular niche and maternal vascular morphogenesis.

developmental biology↗

bioRxiv2019

BACH family members regulate angiogenesis and lymphangiogenesis by modulating VEGFC expression

Angiogenesis and lymphangiogenesis are key processes during embryogenesis as well as under physiological and pathological conditions. Vascular endothelial growth factor C (VEGFC), the ligand for both VEGFR2 and VEGFR3, is a central lymphangiogenic regulator that also drives angiogenesis. Here we report that members of the highly conserved BACH (BTB and CNC homology) family of transcription factors regulate VEGFC expression, through direct binding to its promoter. Accordingly, downregulation of bach2a hinders blood-vessel formation and impairs lymphatic sprouting in a vegfc-dependent manner during zebrafish embryonic development. In contrast, BACH1-overexpression enhances intratumoral blood-vessel density and peritumoral lymphatic vessel diameter in ovarian and lung mouse tumor models. The effects on the vascular compartment correlate spatially and temporally with BACH1 transcriptional regulation of VEGFC expression. Altogether, our results uncover a novel role for the BACH/VEGFC signaling axis in lymphatic formation during embryogenesis and cancer, providing a novel potential target for therapeutic interventions.

developmental biology↗

bioRxiv2019

BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows

Automated image analysis has become key to extract quantitative information from scientific microscopy bioimages, but the methods involved are now often so refined that they can no longer be unambiguously described using written protocols. We introduce BIAFLOWS, a software tool with web services and a user interface specifically designed to document, interface, reproducibly deploy, and benchmark image analysis workflows. BIAFLOWS allows image analysis workflows to be compared fairly and shared in a reproducible manner, safeguarding research results and promoting the highest quality standards in bioimage analysis. A curated instance of BIAFLOWS is available online; it is currently populated with 34 workflows that can be triggered to process image datasets illustrating 15 common bioimage analysis problems organized in 9 major classes. As a complete case study, the open benchmarking of 7 nuclei segmentation workflows, including classical and deep learning techniques, was performed on this online instance. All the results presented can be reproduced online.

bioinformatics↗