Biology subjects

Bombin, S.

Publications and source records attributed to Bombin, S..

9 recordsLinked to original sources

bioRxiv2026

Multi-compartment immune and tumor cell reprogramming by IFNa2 overcomes colon cancer immunotherapy resistance

Approximately 85-90% of colorectal cancers (CRC) are microsatellite stable and resist immune checkpoint inhibitors (ICI). The recent success of intismeran, a lipid nanoparticle (LNP)-delivered mRNA encoding patient-specific tumor antigens, enhances pembrolizumab responses, showing that LNP-delivered nucleic acids can render ICI-resistant tumors responsive by supplying what the tumor microenvironment lacks. Because an IFN-responsive phenotype predicts CRC response to checkpoint blockade and tumor cell PD-L1 represses IFN-I, we asked whether delivering the missing cytokine, rather than antigen, achieves the same conversion. Here we show that PD-1 blockade failed even when initiated before tumor seeding, yet deleting tumor cell PD-L1 abolished colon cancer lung metastasis, implicating a tumor-intrinsic PD-L1 function that antibody blockade does not neutralize. An LNP-encapsulated IFN2-encoding nanoplasmid (LNP-IFN2) transfected tumor cells within lung metastases, converting them into a self-sustaining and tumor-restricted IFN2 source. LNP-IFN2 suppressed colon cancer lung metastasis in syngeneic and humanized mouse models and sensitized these ICI-resistant tumors to PD-1 blockade. Efficacy improved further with neutralization of co-induced IL6. scRNA-Seq revealed multi-compartment reprogramming: SPP1+ macrophages acquired apoptotic signatures as IFN-responsive monocytes replaced them, progenitor-exhausted T cells exited quiescence and expanded, and tumor cells exited a high-cycling state, gained antigen presentation, and shifted away from cuproptosis resistance. The treated microenvironment transcriptionally recapitulated pembrolizumab-responder signatures, positioning LNP-IFN2 as an off-the-shelf nanomedicine for ICI-resistant CRC.

immunology↗

bioRxiv2026

B cell-intrinsic IRF8 transcriptionally reprograms antigen presentation to sustain CD8⁺ T cell antitumor immunity

Interferon regulatory factor 8 (IRF8) is a master transcription factor of myeloid differentiation, but whether IRF8 intrinsically controls B cell function in tumors remains unknown. Using paired single-cell transcriptomic and chromatin accessibility profiling of tumors from wild-type and Irf8-deficient mice, we identify a B cell-intrinsic IRF8 axis regulating antigen presentation and sustaining anti-tumor CD8 T cell immunity. IRF8 establishes conserved chromatin accessibility programs across myeloid cells and plasmablasts centered on antigen processing and MHC class I presentation, but engages distinct motifs by lineage: myeloid cells preferentially utilize ISRE and ETS-composite elements, whereas plasmablasts are selectively enriched for EICE elements, reflecting B lineage-specific IRF8-IRF4 cooperation. Loss of IRF8 disrupts these programs, skews B cells toward plasmablast differentiation and reduces antigen presentation machinery. B cell depletion accelerated tumor growth, while CD40 agonism activated B cells, expanded T cells, and enhanced anti-tumor immunity. B cell-specific IRF8 deletion alone accelerated tumor growth, establishing a cell-intrinsic requirement independent of myeloid IRF8 function. The IRF8-regulated B cell signature was enriched in PD-1 blockade cancer patient responders, and plasmablast abundance correlated with response in pembrolizumab-treated cancer patients. These findings establish IRF8 as a lineage-adapted regulator of antigen presentation and define the IRF8-B cell axis as a determinant of anti-tumor immunity. HighlightsIRF8 establishes a conserved chromatin accessibility across tumor-infiltrating myeloid and B cells Myeloid cells engage ISRE motifs, whereas plasmablasts rely on EICE motifs as IRF8 lineage-specific cis-regulation IRF8 regulates an antigen presentation in B cells to sustain anti-tumor T cell immunity B cell-intrinsic IRF8 transcription signature predicts patient response to PD-1 blockade immunotherapy

immunology↗

bioRxiv2026

Multi-gene biomarkers reveal spatial organization and subpopulation-specific damage response in intrahepatic biliary epithelial cells

Background & AimsIntrahepatic biliary epithelial cell (BEC) heterogeneity remains challenging to define. Here, we sought to identify BEC subpopulations and biomarkers in mouse liver. MethodsWe performed scRNA-seq on Sox9EGFP+ liver epithelium from mice subjected to bile duct ligation (BDL) and sham controls. A machine learning algorithm, NSForest, identified minimal, multi-gene signatures for BEC subpopulations. These "metagenes" were validated using hybridization chain reaction (HCR) FISH in tissue sections from wild-type mice and on primary BECs expanded in vitro. Metagenes were used to match BDL subpopulations to their corresponding sham subpopulations for differential gene expression (DGE) analysis. ResultsWe identified 4 BEC subpopulations in sham controls, each associated with 1-2 gene metagenes. Spatial localization of metagene-defined BEC subpopulations by HCR FISH revealed heterogeneous cellular composition of intrahepatic bile ducts. BECs belonging to a given subpopulation were most likely to have neighbors of the same identity, forming homogenous cellular compartments within ducts. BDL downregulated subpopulation-specific genes and upregulated a damage-associated gene set. BDL samples also included a proliferative subpopulation not found in sham controls, which contained populations enriched for three of the four metagenes. All BEC subpopulations were also found in monolayers in vitro, where they clustered spatially with BECs of the same subtype. ConclusionsNovel metagene biomarkers of BEC subpopulations facilitated spatial localization of BECs in situ, identified subpopulation specific injury responses, and confirmed that BEC heterogeneity is preserved in vitro. The presence of locally homogenous BEC "neighborhoods" in vitro suggests some degree of BEC organization may be epithelial-autonomous.

cell biology↗

bioRxiv2025

Tet1 safeguards lineage allocation in intestinal stem cells

Intestinal stem cells (ISCs) balance self-renewal and differentiation to maintain the intestinal epithelial barrier, which is replaced weekly throughout adult life. Genetic control of ISC differentiation is well-defined relative to transcription factor (TF) activity, but less is known regarding the role of chromatin regulation in ISC biology. Prior work from our lab and others has shown that Tet1, a chromatin modifying enzyme involved in DNA demethylation, is specifically enriched in ISCs and early secretory progenitors. While constitutive loss of Tet1 is associated with defects in early postnatal ISC development, its role in adult ISC biology remains unknown. Here, we show that Tet1 safeguards ISC fate decisions by reducing sensitivity to extrinsic signaling. Inducible, intestine-specific Tet1 knockout mice (Tet1iKO) exhibit environmentally sensitive phenotypes, including absorptive differentiation bias and premature expression of mature absorptive transcripts in ISCs. These phenotypes are largely "silenced" in animals housed in a high-level barrier facility, where Tet1iKO epithelium closely resembles controls. Despite the lack of baseline phenotype in these conditions, Tet1iKO mice retain increased sensitivity to pro-differentiation signaling. In vivo, succinate administration induces increased tuft and goblet cell hyperplasia in the absence of Tet1, while Tet1iKO organoids cultured with IL-4 or DAPT exhibit increased tuft and enteroendocrine cell specification, respectively. While ATAC-seq of Tet1iKO ISCs reveals minimal changes in chromatin accessibility, footprinting analysis suggests increased binding of lineage-specific TFs and CTCF even in the absence of cellular phenotypes. Together, our data demonstrate that Tet1 serves as a "buffer" against ISC differentiation and suggest that it does so in a lineage agnostic manner that is not dependent on changes in chromatin accessibility.

cell biology↗

bioRxiv2025

Quantitative 3D imaging of mouse and human intrahepatic bile ducts in homeostasis and liver injury

Intrahepatic bile ducts (IHBDs) form a complex hierarchical network essential for liver function. Remodeling and expansion of this network during ductular reaction (DR) is a hallmark of liver disease that can be a key indicator of disease severity. Conventional histology fails to capture the full extent of IHBD structural changes following injury due to the complex 3D organization of the IHBD network which limits understanding of DR, especially in human tissue. A major barrier to leveraging 3D imaging as a diagnostic tool is the absence of standardized pipelines for IHBD imaging and analysis. Here, we establish a robust 3D IHBD imaging and analysis workflow and apply it to both mouse and human liver tissues. This pipeline enables quantification of tissue and individual duct ("segment") level features and identifies features of invasive and noninvasive DR. In mouse models, we uncover regional phenotypes, including IHBD diverticula following duct blockage and the formation of anastomosed clusters after hepatocellular injury. Finally, we apply our 3D imaging and analysis workflow to quantify IHBD networks in human liver tissue. This work deepens our understanding of IHBD architecture in homeostasis and injury and lays the groundwork for advanced phenotyping of IHBD morphologies in mice and humans with relevance to next-generation experimental and diagnostic approaches to liver disease.

pathology↗

bioRxiv2024

Sox9 links biliary maturation to branching morphogenesis

Branching morphogenesis couples cellular differentiation with development of tissue architecture. Intrahepatic bile duct (IHBD) morphogenesis is initiated with biliary epithelial cell (BEC) specification and eventually forms a heterogeneous network of large ducts and small ductules. Here, we show that Sox9 is required for developmental establishment of small ductules. IHBDs emerge as a webbed structure by E15.5 and undergo morphological maturation through 2 weeks of age. Developmental knockout of Sox9 leads to decreased postnatal branching morphogenesis, manifesting as loss of ductules in adult livers. In the absence of Sox9, BECs fail to mature and exhibit elevated TGF-{beta} signaling and Activin A. Activin A induces developmental gene expression and morphological defects in BEC organoids and represses ductule formation in postnatal livers. Our data demonstrate that adult IHBD morphology and BEC maturation is regulated by the Sox9-dependent formation of precursors to ductules during development, mediated in part by downregulation of Activin A.

developmental biology↗

bioRxiv2021

Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host:microbiota interactions between clinical obesity classifications. We performed 16S rDNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-24.9), overweight (BMI 25-29.9), or obese (BMI [≥]30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with hosts metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure, and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease. IMPORTANCEObesity is a worldwide epidemic that is associated with a wide range of health issues. Microbiota were shown to influence metabolism and obesity development. Our study aimed to evaluate the interactions between obesity, salivary and fecal microbiota, and metabolite concentrations in healthy individuals. The oral bacterial community was more impacted by the obesity status of the host than fecal microbiota. Consistently for oral and fecal microbiota, the number of strong interactions between bacteria increased with the increase in the obesity status. Several predicted microbial metabolic pathways that were shown to be associated with metabolic health were uniquely enriched between obesity groups. In addition, these metabolic pathways were correlated with plasma and stool metabolites. Our results suggest that oral microbiota might better reflect the obesity status of the host than fecal microbiota, and that correlations between microbial taxa are altered during obesity.

microbiology↗

bioRxiv2021

Symbiotic bacterial community of Drosophila melanogaster changes with nutritional modifications of the diet but can alleviate negative effects on larval phenotypes

Obesity is an increasing pandemic and is caused by multiple factors including genotype, psychological stress, and gut microbiota. Our project investigated the effects produced by high fat and high sugar dietary modifications on microbiota and metabolic phenotype of Drosophila melanogaster. Larvae raised on the high fat and high sugar diets exhibited bacterial communities that were compositionally and phylogenetically different from bacterial communities of the larvae raised on normal diets, especially if parental microbiota were removed. Several of the dominant bacteria taxa that are commonly associated with high fat and high sugar diets across model organisms and even human populations showed similar pattern in our results. Corynebacteriaceae and Erysipelotrichaceae were connected with high fat food, while Enterobacteriaceae and Lactobacillaceae were associated with high sugar diets. In addition, we observed that presence of symbiotic microbiota often mitigated the effect that harmful dietary modifications produced on larvae, including elevated triglyceride concentrations and was crucial for Drosophila survival, especially on high sugar peach diets.

microbiology↗

bioRxiv2020

Influence of the lab adopted natural diet, environmental, and parental microbiota on life history and metabolic phenotype of Drosophila melanogaster larvae.

Obesity is an increasing worldwide epidemic and contributes to physical and mental health losses. The development of obesity is caused by multiple factors including genotype, hormonal misregulation, psychological stress, and gut microbiota. Our project investigated the effects produced by microbiota community, acquired from the environment and horizontal transfer, on traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster from ten, wild-derived genetic lines (DGRP) on naturally fermented peaches, thereby preserving genuine microbial conditions. Our results indicated that larvae raised on the natural and standard lab diets were significantly different from each other in every tested phenotype. In addition, sterilized larvae raised on the autoclaved peach diet, therefore exposed to natural nutritional stress but lacking natural microbiota community, were associated with adverse phenotypes such as low survival rate, longer developmental time, smaller weight, and elevated triglyceride and glucose levels. Our findings suggested that frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development of Drosophila larvae. The presence of parental microbiota did not produce a significant effect on any of the tested phenotypes when larvae were raised on the lab diet. Contrarily, on the peach diet, the presence of parental microbiota increased the weight and development rate, even if the original peach microbiota were still present. In addition, we found that larvae raised on the peach diet formed a microbial community distinctive from larvae raised on the lab or peach autoclaved diets. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.

microbiology↗