Biology subjects

Monti, S.

Publications and source records attributed to Monti, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Age-based shifts in multicellular community organization and abundance in HPV-Negative Head and Neck Cancer

Aging represents a fundamental driver of cancer risk and progression, yet the mechanisms by which aging reshapes the tumor microenvironment remain incompletely understood. To interrogate how aging alters cellular and microenvironmental organization in cancer, we developed an integrated single-cell atlas of HPV-negative head and neck squamous cell carcinoma (HNSCC) encompassing 73 patients aged 18-91 years. Using a multi-layered computational framework combining NMF-based module discovery and partial correlation network analysis, we reveal that age-associated differences in tumor composition are driven primarily by selective shifts in cell type abundance and organization rather than widespread age-dependent transcriptional rewiring. We identify an age-enriched cellular community centered on basal-like squamous epithelial states linked to epithelial-mesenchymal transition, matrix-associated myofibroblast-like CAFs, and FOLR2+ macrophages, which secrete immunosuppressive and ECM-remodeling factors. Cross-dataset in-silico validation via TCGA transcriptomes, spatial transcriptomics, and mouse tumor models confirms the correlation of these cell types across patients, specific ligand-receptor usage, and increased proportions of epithelial and stromal cells in aged mouse models. Among epithelial cell-intrinsic age-associated transcriptional changes, midkine (MDK) emerges as a rare but robust tumor-derived signal linked to stromal remodeling, immunosuppression, and invasive epithelial programs. These findings reveal conserved mechanisms of age-dependent cellular reorganization in the tumor microenvironment and identify MDK and associated stromal-remodeling pathways as potential intervention points for age-stratified cancer therapy.

cancer biology↗

bioRxiv2026

Signature Recontextualization: Mapping perturbational signatures across biological contexts

Perturbational transcriptomics is a powerful tool for understanding gene function and drug effects, yet predicting how perturbations manifest across different biological contexts remains a central challenge, limiting translation from model systems to clinically relevant tissues. Despite growing interest in this problem, benchmarking efforts have been hindered by inconsistent evaluation tasks, heterogeneous metrics, and limited assessment across perturbation types and biological systems. Here, we introduce a benchmarking framework for cross-context perturbation-signature prediction (a task we define as signature recontextualization), grounded in explicit definitions of the prediction task, target-data availability, and evaluation metrics centered on signature recovery. The framework evaluates prediction performance across three target-context data regimes: (1) control only, where only control profiles from the target context are measured; (2) low coverage, where a limited subset of perturbations in the target context are measured; and (3) high coverage, where most perturbations in the target context are measured. This design enables systematic assessment of how prediction performance depends on target-context sample size while providing a standardized basis for comparing methods. We evaluate newly developed projection-based (projectCor) and network-based (netProp) methods alongside deep learning-based foundation models (scGPT, STACK) and statistical baselines. The benchmark spans four diverse perturbational datasets: CRISPR knockdowns and drug perturbations in cell lines, plus in vivo chemical perturbations in rat tissues from DrugMatrix, extending evaluation beyond isolated cell-line models to tissue-level responses. Across tasks, projection and network propagation approaches show strong flexibility across perturbation types and biological contexts, and in several cases match or exceed the performance of deep learning and foundation models, suggesting that model complexity does not inherently improve cross-context generalization. We further show that perturbation predictability varies substantially with pathway conservation, transcriptional response strength, and baseline similarity between source and target contexts. All datasets, methods, and evaluation utilities are released as an open-source R package (sigRecon), providing a foundation for reproducible benchmarking and future method development.

bioinformatics↗

bioRxiv2026

Environmental chemical mixtures reprogram mammary epithelial development to epigenetic states associated with breast cancer

Environmental exposures occur as complex mixtures, yet the mechanisms by which they alter human tissue development and confer cancer susceptibility remain poorly defined. Here, we establish a physiological 3D human breast organoid high-content screening (3D-HCS) platform that quantitatively links exposure-induced developmental disruption to cancer-relevant cell states. Screening of structurally diverse environmental chemicals as single agents but also as mixtures reveals heterogeneous but reproducible developmental responses, indicating that distinct environmental chemicals perturb different aspects of mammary morphogenesis. Focusing on bisphenols, we show that a physiological-dose mixture (BPA, BPS, and BPF; 3BPX) disrupts organoid development and induces transcriptional programs characterized by extracellular matrix remodeling, epithelial plasticity, and partial epithelial-mesenchymal transition (EMT), accompanied by widespread DNA methylation remodeling. The 3BPX exposure signature maps to ER luminal breast cancers and is preferentially enriched in invasive lobular carcinoma (ILC), a subtype characterized by epithelial plasticity and stromal interaction. Genome-wide DNA methylation profiling revealed that the 3BPX-associated methylation signature is detectable in primary tumors and adjacent normal tissue and is enriched in Normal-like tumors and ILC. Together, these findings demonstrate that environmentally relevant chemical exposures induce heterogeneous developmental perturbations that converge on conserved transcriptional and epigenetic programs associated with epithelial plasticity, tissue remodeling, and cancer susceptibility. These exposure-induced states persist as molecular "scars" that map to defined epithelial and stromal compartments in human breast cancers, supporting a model in which developmental exposures establish a field of increased oncogenic potential. Summary StatementUsing a human breast organoid high-content screening platform, we show that real-world chemical mixtures induce heterogeneous developmental disruption that converges on conserved EMT, wound-response, and epigenetic programs. These exposure-induced states persist as molecular "scars" and map to specific epithelial and stromal compartments in human breast cancers, particularly invasive lobular carcinoma, suggesting a developmental origin of cancer susceptibility.

cancer biology↗

bioRxiv2025

hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models

Enrichment analysis is a cornerstone of "omics" data interpretation, enabling researchers to connect analysis results to biological processes and generate testable hypotheses. While well-established tools exist for transcriptomics and other omics layers, the development of robust enrichment resources for metabolomics remains comparatively limited. To address this gap, we developed hypeR-GEM, a methodology and associated R package that adapts gene set enrichment analysis to metabolomics. hypeR-GEM leverages genome-scale metabolic models (GEMs) to infer reaction-based links between metabolites and enzyme-coding genes, enabling the mapping of metabolite signatures to gene signatures and their subsequent annotation via gene set enrichment analysis. We validated hypeR-GEM using paired metabolomics-proteomics and metabolomics-transcriptomics datasets by assessing whether genes mapped from metabolites significantly overlapped with differentially expressed proteins or transcripts. We further evaluated whether pathways enriched via hypeR-GEM-mapped genes corresponded to those derived from paired proteomic or transcriptomic data. In most datasets analyzed, both the predicted enzyme-coding genes and the associated enriched pathways showed significant concordance with independently derived omics signatures, supporting the utility and robustness of hypeR-GEM. Finally, we applied hypeR-GEM to the analysis of age-associated metabolic signatures from the New England Centenarian Study. The results revealed consistent enrichment of lipid-related pathways, aligning with the well-established role of lipid metabolism in aging, and highlighted additional pathways not captured in the metabolites annotation, demonstrating hypeR-GEMs practical utility in a real-world use case.

bioinformatics↗

bioRxiv2025

Metabolic medications modify prostate cancer progression through exosome reprogramming

Among prostate cancer patients, co-morbid Type 2 Diabetes (T2D) is associated with faster progression to biochemical recurrence and increased risk of mortality. Previous work from our lab provides evidence that exosomes purified from media of insulin resistant adipocytes or T2D patient plasma likely drives these outcomes by delivering miRNAs that exacerbate tumor aggressiveness in several breast and prostate cancer models. Here, we build on our previous findings to investigate whether treatment with metabolic medications attenuates the tumor promoting effects of exosomes. We found that human DU145 cells, a model for prostate cancer, treated with plasma exosomes from T2D patients, shows patterns in global gene transcription that resolve by patient treatment with metformin. To test the effects of metformin experimentally, we used a murine model of insulin resistance (IR). Treating DU145 cells with miRNAs purified from the plasma exosomes of IR mice, we found that cells transfected with miRNAs from the metformin-treated IR group displayed significantly less migration than cells transfected with miRNAs from the unmedicated IR group. We suggest that metformin may partially reverse effects of T2D to exacerbate tumor aggressiveness by modifying the miRNA payload of plasma exosomes.

cancer biology↗

bioRxiv2025

Dietary Serine Restriction Impacts H3K27 and H3K4 Methyl Epigenomes to Impede Head and Neck Cancer Cell Plasticity and Tumor Growth

Oral squamous cell carcinoma (OSCC) is an aggressive head and neck malignancy characterized by high morbidity, therapeutic resistance and intratumoral heterogeneity driven by plastic cell states. Given that metabolic inputs can shape cell identities via epigenetic mechanisms, we investigated how metabolism of a non-essential amino acid, serine, affects histone modifications with key roles in cell plasticity: H3K27me3, which represses differentiation genes, and H3K4me3 which activates stemness and epithelial-to-mesenchymal transition (EMT) genes. Using a panel of human OSCC patient-derived cell lines and an orthotopic murine isograft model, we show that OSCC cells depend on exogenous serine for proliferation. Dietary serine deprivation induced de novo serine synthesis with a concomitant increase in -ketoglutarate (KG), a cofactor for KDM6B and KDM5A/B demethylases of H3K27me3 and H3K4me3, respectively. RNA-seq-derived serine deprivation gene signatures revealed activation of keratinization program and suppression of EMT and proliferation genes and tracked with good OSCC patient outcomes in TCGA. Furthermore, CUT & RUN profiling showed site-specific losses of H3K27me3 at differentiation genes and reduction of H3K4me3 at stemness, EMT and cell cycle genes. However, inhibition of KG with 2-hydroxyglutarate was not sufficient to rescue cell proliferation. Instead, genome-wide analysis revealed widespread H3K27me3-H3K4me3 bivalency, with extensive transcriptional repression of proliferation and oncogenic programs. Functionally, serine deprivation impaired orthotopic tumor growth and improved the immune landscape in syngeneic mice. Our studies identify a metabolic serine-KG-KDM-H3K27me3/H3K4me3 bivalency axis that globally reprograms OSCC chromatin as a potential therapeutic strategy to impede tumor plasticity and evolution to advanced disease. ImplicationsThis study identifies the tumor-suppressive role of dietary serine deprivation through epigenetic reprogramming of chromatin in OSCC.

cancer biology↗

bioRxiv2025

IPSC-based modeling of resiliency in centenarians reveals longevity-specific signatures

Centenarians represent a human model of resilience to age-related decline, yet resiliency mechanisms remain elusive. Here, we establish an induced pluripotent stem cell (iPSC)-based platform to interrogate resilience signatures in centenarians. IPSC-derived neurons from centenarians exhibit transcriptional programs promoting synaptic integrity, calcium homeostasis, and cholesterol biosynthesis, while suppressing proteostatic stress pathways. Functionally, these neurons maintain stable calcium dynamics, reduced baseline mitochondrial activity, and energy-efficient homeostasis. Upon challenge, centenarian-derived neurons mount a robust stress response, in contrast to attenuated responses in non-centenarian controls. This resilience signature parallels adaptations in long-lived mammals and aligns with healthy brain aging, while showing erosion in Alzheimers disease and cancer. Our platform provides a scalable human model for dissecting resilience biology offering a framework to extend healthspan and mitigate age-related decline.

molecular biology↗

bioRxiv2025

METABOLOMIC SIGNATURES OF EXTREME OLD AGE: FINDINGS FROM THE NEW ENGLAND CENTENARIAN STUDY

The New England Centenarian Study (NECS) provides a unique resource for the study of extreme human longevity (EL). To gain insight into biological pathways related to EL, chronological age and survival, we used an untargeted serum metabolomic approach (> 1,400 metabolites) in 213 NECS participants, followed by integration of our findings with metabolomic data from four additional studies. Compared to their offspring and matched controls, EL individuals exhibited a distinct metabolic profile characterized by higher levels of primary and secondary bile acids - most notably chenodeoxycholic acid (CDCA) and lithocholic acid (LCA) - higher levels of biliverdin and bilirubin, and stable levels of selected steroids. Notably, elevated levels of both bile acids and steroids were associated with lower mortality. Several metabolites associated with age and survival were inversely associated with metabolite ratios related to NAD+ production and/or levels (tryptophan/kynurenine, cortisone/cortisol), gut bacterial metabolism (ergothioneine/ trimethylamine N-oxide, aspartate/quinolinate), and oxidative stress (methionine/methionine sulfoxide), implicating these pathways in aging and/or longevity. We further developed a metabolomic clock predictive of biological age, with age deviations significantly associated with mortality risk. Key metabolites predictive of biological aging, such as taurine and citrate, were not captured by traditional age analyses, pointing to their potential role as biomarkers for healthy aging. These results highlight metabolic pathways that may be targeted to promote metabolic resilience and healthy aging.

systems biology↗

bioRxiv2025

Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies

Although aging is a universal event, some individuals are able to achieve extreme longevity. The Long-Life Family Study (LLFS) enrolls participants from families enriched with long-lived individuals, serves as a valuable dataset for studying ageing phenotypes and identify potential intervention targets. We analyzed the association between age at blood draw and 16,284 RNAseq-based blood transcriptomic data from 2,167 LLFS participants with ages ranging from 18 to 107, replicated the results in the Integrative Longevity Omics Study (ILO) dataset of 20,884 RNAseq-based blood transcriptomic data from 419 participants, with ages ranging from 60 to 108, and further compared our findings to a published reference aging signature. We identified 4,227 transcripts increasing and 4,044 transcripts decreasing with age, and enrichment analysis revealed age-related upregulation of inflammatory and senescence-related pathways, and downregulation of MYC and Wnt/{beta}-catenin targets, among others. Further, a subset of transcripts showed age associations unique to the longevity-enriched cohorts (LLFS and ILO). We also identified 314 transcripts significantly associated with mortality risk and found that pro-survival gene sets included NK cell-mediated cytotoxicity and GPCR signaling. Finally, increased transcriptomic age predicted using transcriptomic clock was strongly associated with increased mortality. In summary, this study identified robust transcriptomic signatures of aging and mortality in a longevity-enriched population, highlighting key biological pathways such as immune modulation, inflammation, and senescence. Authors notesThis manuscript has been peer-reviewed and accepted by GeroScience (Springer). This bioRxiv article reflects the published version, incorporating revisions made in response to reviewers comments. The main content, results, and conclusions remain unchanged from the previous version, while the Discussion section has been expanded to further address the functional annotation and clinical relevance of the identified markers. Copy of the acceptance letterThe editors are pleased to inform you that your manuscript, JAAA-D-25-01946R1 entitled "Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies" has been accepted for publication in GeroScience as an Original Article. The editors commend you on your outstanding contribution to the journal. Your manuscript can be published online ahead of print within approximately two weeks.

molecular biology↗

bioRxiv2025

Robust Serum Proteomic Signatures of APOE2

We previously identified a signature of 16 serum proteins that highlighted a role of the e2 allele of APOE in lipid regulation via apolipoprotein B (APOB) and apolipoprotein E (APOE), and in inflammation. The serum proteins were profiled using the aptamer-based Somalogic technology. Here, we validate and expand the serum protein signature of APOE using a combination of mass-spectrometry, ELISA, Luminex, antibody-based Olink proteomics, and blood transcriptomics. We replicate the association between APOB and the e2 allele of APOE, we correct the pattern of association between APOE genotypes and serum level of APOE, and we detect new associations between APOE genotypes and the complex of apolipoproteins APOC1, APOC4, APOC2, APOC3, APOE, APOF and APOL1. In addition, we discover 13 new proteins that correlate with APOE genotypes. This extended signature includes granule proteins CAMP, CTSG, DEFA3, and MPO secreted from neutrophils and points to olfactomedin 4 (OLFM4) as a new target for the prevention of Alzheimers disease.

genetics↗

bioRxiv2025

Sub-phenotypes of pneumonia defined by pulmonary histopathological features

Establishing sub-phenotypes of pneumonia based on distinct host processes will be a step towards using host-directed therapies (to complement microbe-directed therapies) more rationally and precisely. Although pneumonia is a pulmonary pathophysiology, histological changes within the lungs have not been leveraged for sub-phenotyping. We addressed this by scoring 18 histopathology features (e.g., type 2 cell hyperplasia or necrosis) across rapid autopsy lung samples from 276 elderly subjects with pneumonia. Machine learning algorithms segregated subjects into seven different sub-phenotypes of pneumonia with distinct histopathology signatures. Quantitative immunofluorescence demonstrated associations of macrophages, neutrophils, T cells, and B cells with select histology features and pulmonary pathology sub-phenotypes. Mouse models revealed corollary sub-phenotypes, although some histology features observed in human lungs were never observed in mice. By illuminating this spectrum of histopathologies and discriminating discrete sub-phenotypes of pneumonia, a foundational framework emerges for developing and using host-directed therapies for subsets of pneumonia patients.

immunology↗

bioRxiv2025

LSD1 inhibition corrects dysregulated MHC-I and dendritic cells activation through IFNγ-CXCL9-CXCR3 axis to promote antitumor immunity in HNSCC

Poor infiltration of CD8+ T cells and dysregulated MHC-I confer resistance to anticancer clinical therapies. This study aimed to elucidate the mechanisms of lysine-specific demethylase 1 (LSD1, encoded by KDM1A gene) in antitumor immunity in Head and Neck Squamous cell carcinoma (HNSCC). LSD1 inhibition in syngeneic and chronic tobacco carcinogen-induced HNSCC mice recruited activated dendritic cells (DCs), CD4+ and CD8+ T cells, enriched interferon-gamma (IFN{gamma}) in T cells, CXCL9 in DCs, and CXCR3 in T cells, as evaluated using flow cytometry and single-cell RNA-seq analysis. Humanized HNSCC mice and TCGA data validated the inverse correlation of KDM1A with DC markers, CD8+ T cells, and their activating chemokines. Kdm1a knockout in mouse HNSCC and LSD1 inhibitor treatment to co-culture of human HNSCC cells with human peripheral blood mononuclear cells (PBMCs) resulted in MHC-I upregulation in cancer cells for efficient antigen presentation in tumors. Overall, LSD1 inhibition in tumor cells upregulates MHC class I and induces DCs to produce CXCL9, which in turn activates CD8+ T cells through the CXCL9-CXCR3 axis to produce IFN{gamma}. Finally, we identified a novel mechanism by which LSD1 inhibition promotes the activation of H3K4me2 and its direct interaction with MHC-I to induce antitumor immunity. This may have implications in poorly immunogenic and immunotherapy-resistant cancers. Statement of SignificanceLSD1-mediated unique mechanisms have impact on epigenetic therapy, MHC-I resistant HNSCC therapies, and poor CD8+ and dendritic cell infilterated tumors.

cancer biology↗

bioRxiv2025

A highly resolved integrated transcriptomic atlas of human breast cancers

In this study, we developed an integrated single cell transcriptomic (scRNAseq) atlas of human breast cancer (BC), the largest resource of its kind, totaling > 600,000 cells across 138 patients. Rigorous integration and annotation of publicly available scRNAseq data enabled a highly resolved characterization of epithelial, immune, and stromal heterogeneity within the tumor microenvironment (TME). Within the immune compartment we were able to characterize heterogeneity of CD4, CD8 T cells and macrophage subpopulations. Within the stromal compartment, subpopulations of endothelial cells (ECs) and cancer associated fibroblasts (CAFs) were resolved. Within the cancer epithelial compartment, we characterized the functional heterogeneity of cells across the axes of stemness, epithelial-mesenchymal plasticity, and canonical cancer pathways. Across all subpopulations observed in the TME, we performed a multi-resolution survival analysis to identify epithelial cell states, and immune and stromal cell types, which conferred a survival advantage in both The Cancer Genome Atlas (TCGA), METABRIC, and SCANB. We also identified robust associations between TME composition and clinical phenotypes such as tumor subtype and grade that were not discernible when the analysis was limited to individual datasets, highlighting the need for atlas-based analyses. This atlas represents a valuable resource for further high-resolution analyses of TME heterogeneity within BC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/643025v3_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@4c51d3org.highwire.dtl.DTLVardef@8ffc01org.highwire.dtl.DTLVardef@e9a6f7org.highwire.dtl.DTLVardef@1d0c058_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer

Head and Neck Squamous Cell Carcinomas (HNSCC) are the seventh most prevalent form of cancer and are associated with human papilloma virus infection (HPV-positive) or with tobacco and alcohol use (HPV-negative). HPV-negative HNSCCs have a high recurrence rate, and individual patients responses to treatment vary greatly due to the high level of cellular heterogeneity of the tumor and its microenvironment. Here, we describe a HNSCC single cell atlas, which we created by integrating six publicly available datasets encompassing over 230,000 cells across 54 patients. We contextualized the relationships between existing signatures and cell populations, identified new subpopulations, and show the power of this large-scale resource to robustly identify associations between transcriptional signatures and clinical phenotypes that would not be possible to discover using fewer patients. We reveal a previously undefined myeloid population, sex-associated changes in cell type proportions, and novel interactions between CXCL8-positive fibroblasts and vascular endothelial cells. Beyond our findings, the atlas will serve as a public resource for the high-resolution characterization of tumor heterogeneity of HPV-negative HNSCC.

cancer biology↗

bioRxiv2025

Pde5a Deficiency Prevents Diet-Induced Obesity via Adipose cAMP-PKA Activation Enhancing Fat Browning

Cyclic nucleotides are critical regulators of adaptive thermogenesis and adipogenesis, with their intracellular levels finely tuned by phosphodiesterases. Phosphodiesterase type 5 (PDE5A) modulates cyclic guanosine monophosphate levels in adipocytes. While PDE5A inhibition has shown promise in patients with diabetes, its role in metabolism remains unclear. Using Pde5a knockout mouse models, we demonstrated that mice lacking Pde5a exhibit enhanced browning of white adipose tissue and reduced hepatic fat content. Following high-fat diet, Pde5a-/- mice are resistant to obesity, displaying improved glucose metabolism and enhanced thermogenesis. These protective effects stem from an early developmental knockdown of Pde5a, leading to a metabolic reprogramming driven by cAMP-PKA pathway activation. The convergence of cGMP and cAMP signaling orchestrates thermogenic and systemic metabolic adaptations. Our findings establish PDE5A as a novel regulator of energy homeostasis, suggesting its inhibition as a valuable adjuvant therapy for metabolic disorders.

cell biology↗

bioRxiv2024

Plasma Exosomes in Insulin Resistant Obesity Exacerbate Progression of Triple Negative Breast Cancer

Breast cancer, the most common cancer among women worldwide, continues to pose significant public health challenges. Among the subtypes of breast cancer, triple-negative breast cancer (TNBC) is particularly aggressive and difficult to treat due to the absence of receptors for estrogen, progesterone, or human epidermal growth factor receptor 2, rendering TNBC refractory to conventional targeted therapies. Emerging research underscores the exacerbating role of metabolic disorders, such as type 2 diabetes and obesity, on TNBC aggressiveness. Here, we investigate the critical cellular and molecular factors underlying this link. We explore the pivotal role of circulating plasma exosomes in modulating the tumor microenvironment and enhancing TNBC aggressiveness. We find that plasma exosomes from diet-induced obesity mice induce epithelial-mesenchymal transition features in TNBC cells, leading to increased migration in vitro and enhanced metastasis in vivo. We build on our previous reports demonstrating that plasma exosomes from obese, diabetic patients, and exosomes from insulin-resistant 3T3-L1 adipocytes, upregulate key transcriptional signatures of epithelial-mesenchymal transition in breast cancer. Bioinformatic analysis reveals that TNBC cells exhibit higher expression and activation of proteins related to the Rho-GTPase cascade, particularly the small Ras-related protein Rac1. Our approach suggests novel therapeutic targets and exosomal biomarkers, ultimately to improve prognosis for TNBC patients with co-morbid metabolic disorders.

cancer biology↗

bioRxiv2024

Plasma exosomes from individuals with type 2 diabetes drive breast cancer aggression in patient-derived organoids

Women with obesity-driven diabetes (T2D) are predisposed to more aggressive breast cancers, yet patient metabolic status does not fully inform current standards of care. We previously identified plasma exosomes as key mediators of intercellular communication and drivers of tumor progression; however, their effect on immune cells within the tumor microenvironment (TME) remains unclear. To model this exosomal signaling, we developed a novel method to generate patient-derived organoids (PDOs) from breast tumor resections, uniquely preserving native tumor-infiltrating lymphocytes (TILs) for the first time. This modifiable and reproducible system provides a robust platform for studying human tumor-immune interactions within the TME in vitro. After 3-day exosome treatment, we assessed the impact of T2D-derived exosomes on PDOs via single-cell RNA sequencing. Exosomes from T2D patient plasma triggered a 13.6-fold expansion of immunosuppressive TILs compared to non-diabetic exosome controls. This immune dysfunction may permit the survival of micrometastases and undermine immune checkpoint therapies, a known challenge for cancer patients with comorbid T2D. Tumor-intrinsic analysis revealed a 1.5-fold increase in intratumoral heterogeneity and approximately 2.3-fold upregulation of epithelial-to-mesenchymal transition, invasiveness, and cancer stemness, consistent with enhanced tumor aggressiveness and metastatic potential of these PDOs. These findings demonstrate how metabolic dysregulation in T2D disrupts tumor-immune crosstalk, profoundly impairing anti-tumor immunity and driving cancer progression through a previously underappreciated exosomal signaling pathway. These insights into the TME could inform personalized treatments for patients with this comorbidity.

cancer biology↗

bioRxiv2024

The Aryl Hydrocarbon Receptor Controls IFNγ-Induced Immune Checkpoints PD-L1 and IDO via the JAK/STAT Pathway in Lung Adenocarcinoma

While immunotherapy has shown efficacy in lung adenocarcinoma (LUAD) patients, many respond only partially or not at all. One limitation in improving outcomes is the lack of a complete understanding of immune checkpoint regulation. Here, we investigated a possible link between an environmental chemical receptor implicated in lung cancer and immune regulation, (the aryl hydrocarbon receptor/AhR), a known but counterintuitive mediator of immunosuppression (IFN{gamma}), and regulation of two immune checkpoints (PD-L1 and IDO). AhR gene-edited LUAD cell lines, a syngeneic LUAD mouse model, bulk- and scRNA sequencing of LUADs and tumor-infiltrating leukocytes were used to map out a signaling pathway leading from IFN{gamma} through the AhR to JAK/STAT, PD-L1, IDO, and tumor-mediated immunosuppression. The data demonstrate that: 1) IFN{gamma} activation of the JAK/STAT pathway leading to PD-L1 and IDO1 upregulation is mediated by the AhR in murine and human LUAD cells, 2) AhR-driven IDO1 induction results in the production of Kynurenine (Kyn), an AhR ligand, which likely mediates an AhRIDO1KynAhR amplification loop, 3) transplantation of AhR-knockout LUAD cells results in long-term tumor immunity in most recipients. 4) The 23% of AhR-knockout tumors that do grow do so at a much slower pace than controls and exhibit higher densities of CD8+ T cells expressing markers of immunocompetence, increased activity, and increased cell-cell communication. The data definitively link the AhR to IFN{gamma}-induced JAK/STAT pathway and immune checkpoint-mediated immunosuppression and support the targeting of the AhR in the context of LUAD.

cancer biology↗