Biology subjects

Stanger, B.

Publications and source records attributed to Stanger, B..

12 recordsLinked to original sources

bioRxiv2026

Mono-ADP-ribosylation-driven immunosuppression and cross-resistance to therapy through cancer cell intrinsic and extrinsic mechanisms

Mono-ADP-ribosylation (MARylation) is emerging as an important regulator of anti-cancer immunity and immunosuppressive tumor microenvironment (TME). Our previous studies showed that PARP11, one of several enzymes that facilitate MARylation, regulates the activities of intratumoral cytotoxic T lymphocytes (CTLs) and regulatory T cells (Tregs). Here, we demonstrate that stimuli such as adenosine, epinephrine, or glucagon-like peptide-1 (GLP1) induced PARP11 in cancer cells. Upregulation of PARP11 in cancer cells led to PARP11-mediated MARylation, ubiquitination, and accelerated degradation of MHC-I through the autophagy-lysosomal pathway. Induction of PARP11 protected cancer cells from killing by specific CTLs and stimulated tumor growth and progression. Genetic ablation of PARP11 attenuated MHC-I MARylation, ubiquitination, and interaction with autophagy receptors. Pharmacologic inhibition of PARP11 in pancreatic ductal adenocarcinoma (PDAC) cells restored their MHC-I levels, sensitized them to killing by CTLs, inhibited tumor growth, and impeded their initial resistance to chemotherapy and their acquired resistance to targeted therapy with RAS inhibitors. Moreover, inhibition of PARP11 prevented hyperprogressive disease in a mouse melanoma model treated with immune checkpoint inhibitors (ICBs), suggesting that PARP11 is a major therapeutically actionable driver of immunosuppression in tumors. SYNOPSISInduction of PARP11 in the tumor microenvironment mediates immunosuppression. This study reports that PARP11-driven MARylation and ubiquitination of MHC-I in cancer cells drives immune evasion, tumor growth and resistance to therapies.

cancer biology↗

bioRxiv2026

SPTBN2 promotes an immunosuppressive tumor microenvironment and cross-resistance to anti-cancer therapies

Immunosuppressive tumor microenvironment (TME) inactivates CD8+ cytotoxic lymphocytes (CTLs). Here, we identify SPTBN2 spectrin as a key immunosuppressive regulator induced in CTLs in response to nutritional deficit. In human pancreatic and colorectal cancers, SPTBN2 expression negatively correlated with CTL infiltration and patients survival. In TME of mouse pancreatic and colorectal adenocarcinomas, SPTBN2 inactivated intratumoral CTLs, stimulated tumor growth and conferred cross-resistance to anti-cancer therapies. SPTBN2 knockout protected CAR T-cells from trogocytosis and increased their memory state. SPTBN2 maintained levels of cell surface proteins such as BTLA that undermine CAR T-cell cytotoxicity and promote exhaustion. Re-expression of BTLA largely reversed phenotypes in SPTBN2-deficient CAR T-cells. In manufactured CAR T cells, SPTBN2 was associated with their clinical failure in pediatric patients with leukemia. Accordingly, ablation of SPTBN2 in CAR T-cells increased their cytotoxicity, in vivo persistence and therapeutic effects indicating that SPTBN2 can be targeted to increase the efficacy of anti-cancer therapies.

cancer biology↗

bioRxiv2025

Identification and Implications for Tumor Heterogeneity of a DNA Methylation-Based Signature Classifying Pancreatic Ductal Adenocarcinoma Based on their Cellular Origin

BackgroundPancreatic ductal adenocarcinoma (PDAC) arises from distinct cellular origins, yet the extent to which DNA methylation patterns from normal pancreatic cells are preserved in tumor cells remains unclear. Identifying cell-of-origin signatures may enhance PDAC classification and therapeutic stratification. ObjectiveTo determine whether DNA methylation signatures in normal acinar and ductal pancreatic cells are retained in PDAC cell lines and to develop a robust classifier for distinguishing tumor origins. DesignWe performed DNA methylation profiling using the Illumina Infinium Mouse MethylationEPIC array on normal acinar and ductal cells and their PDAC derivatives in genetically engineered mouse models (GEMMs). Differential methylation analysis, and hierarchical clustering were used to identify and validate a conserved cell-of-origin DNA methylation signature. A logistic regression model was developed for classification. ResultsWe identified 178 CpG sites that remain preserved during tumorigenesis and effectively distinguished acinar- and ductal-derived PDAC cell lines. This signature was validated across independent sample sets, primary tumors, and orthotopic allografts. It successfully classified cell lines of unknown origin, including PDAC samples from KPC mice, and revealed the impact of oncogenic mutations on tumor fate. A logistic regression model supported these findings, confirming the robustness of the classification approach. Furthermore, the cell of origin influenced key PDAC characteristics, including treatment response, highlighting its potential role in molecular subtyping and patient stratification. ConclusionA preserved DNA methylation signature during pancreatic carcinogenesis distinguishes PDAC origins and influences tumor behavior. These results highlight the potential of DNA methylation profiling for tumor classification and personalized treatment strategies. They also raise important questions about the relevance of KPC mice as a preclinical model and the mechanisms driving PDAC heterogeneity. What is already known on this topicO_LIHuman PDAC exhibits significant heterogeneity, with molecular subtyping (classical vs basal-like) providing some insights into tumor behavior and clinical outcomes. C_LIO_LIMouse acinar and ductal cells can give rise to PDAC, influencing tumor characteristics and survival outcomes. C_LIO_LIDNA methylation is a powerful tool for tracing cellular identity and distinguishing cancer subtypes based on epigenetic profiles. C_LI What this study addsO_LIA cell-of-origin methylation signature is preserved during mouse carcinogenesis and across diverse experimental settings, providing a reliable tool for tumor classification. C_LIO_LIA DNA methylation-based classification system reliably distinguishes between acinar- and ductal-origin PDAC, filling a critical gap in methods to trace tumor lineage. C_LIO_LIAcinar- and ductal-derived PDACs exhibit distinct methylation patterns that correlate with differences in tumor behavior, such as chemoresistance, highlighting the biological relevance of cellular origin in PDAC. C_LIO_LIThe study provides new insights into how cell-of-origin influences PDAC heterogeneity and could lead to more precise therapeutic strategies tailored to the tumors lineage. C_LI How this study might affect research, practice or policyO_LIThis study provides a new, reliable method for classifying PDAC based on its cellular origin, which could significantly improve tumor classification in both preclinical and clinical settings, aiding in more accurate diagnoses and prognostic predictions. C_LIO_LIThe identification of distinct methylation patterns linked to tumor behavior offers valuable insights for developing personalized treatment strategies, as therapies could be tailored based on the tumors cellular origin and associated molecular characteristics. C_LIO_LIThe preservation of cell-of-origin methylation signature suggests the potential for developing a universal biomarker for PDAC classification, which could guide future clinical trials, therapeutic targeting, and patient stratification in PDAC care. C_LI

cancer biology↗

bioRxiv2024

Quantitative MRI Measurements Capture Pancreatic Cancer and Stroma Reactions to New KRAS Inhibitor

PurposeIn pancreatic ductal adenocarcinoma (PDAC), KRAS mutations drive both cancer cell growth and formation of a dense stroma. Small molecule KRAS inhibitors (KRASi) represent a promising new treatment hence clinical tools that can assess early response, detect resistance and/or predict prolonged survival are desirable to understand clinical biology of KRASi. We hypothesized that diffusion-weighted MRI (DWI) can detect cell death while dynamic contrast enhanced MRI (DCE) and magnetization transfer ratio (MTR) imaging are sensitive to tumor microenvironment changes, and these metrics shed insights into tumor size change induced by KRASi treatment. Experimental DesignMultiple preclinical PDAC models including a genetically engineered mouse model (KPC) received MRTX1133, a KRASi specific for KRASG12D mutation. Quantitative imaging markers were corroborated with immunohistochemistry (IHC) analyses. ResultsSignificant increase of tumor apparent diffusion coefficient (a DWI metric) was detected as early as 48h and persisted to Day7 after initiation of KRASi treatment and was strongly correlated with cell death and reduced cellularity, resulting in greatly prolonged median survival in treated mice. Capillary perfusion/permeability (a DCE metric) exhibited an inverse relationship with microvascular density. Distinct responses of KRASG12C versus KRASG12D tumors to MRTX1133 were captured by the MRI metrics corroborated with IHC. When tumors developed resistance to MRTX1133, the imaging marker values exhibited a reversal from those of responding tumors. ConclusionsMultiparametric MRI provides early biological insights of cancer and stromal response to KRASi treatment and sets the stage for testing the utility of these clinically ready MRI methods in patients receiving KRASi therapy. Translational relevanceEmerging small molecule KRAS inhibitors (KRASi) represent a new class of therapy for PDAC. Clinical tools that can provide early biological insights of KRASi therapy are desirable. In PDAC models, we examined a clinically ready imaging protocol that combines MRI-based tumor size, diffusion-weighted MRI (DWI), dynamic contrast enhanced MRI (DCE), and magnetization transfer ratio (MTR) for detection of early response as well as acquired resistance to MRTX1133, a KRASi being evaluated in clinical trials. Our data show that DWI and DCE metrics provided key insights of significant cell death and tumor microenvironment changes underlying tumor size regression as early as 48 hours after KRASi treatment initiation. These MRI metrics also captured resistance to KRASi developed over prolonged treatment. This study has high translational relevance by employing clinically applied MRI methods, an investigational new drug and a genetically engineered mouse model that recapitulates salient features of human PDAC.

cancer biology↗

bioRxiv2024

Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity

Endoplasmic reticulum to mitochondria Ca2+ transfer is important for cancer cell survival, but the role of mitochondrial Ca2+ uptake through the mitochondrial Ca2+ uniporter (MCU) in pancreatic adenocarcinoma (PDAC) is poorly understood. Here, we show that increased MCU expression is associated with malignancy and poorer outcomes in PDAC patients. In isogenic murine PDAC models, Mcu deletion (McuKO) ablated mitochondrial Ca2+ uptake, which reduced proliferation and inhibited self-renewal. Orthotopic implantation of MCU-null tumor cells reduced primary tumor growth and metastasis. Mcu deletion reduced the cellular plasticity of tumor cells by inhibiting epithelial-to-mesenchymal transition (EMT), which contributes to metastatic competency in PDAC. Mechanistically, the loss of mitochondrial Ca2+ uptake reduced expression of the key EMT transcription factor Snail and secretion of the EMT-inducing ligand TGF{beta}. Snail re-expression and TGF{beta} treatment rescued deficits in McuKO cells and restored their metastatic ability. Thus, MCU may present a therapeutic target in PDAC to limit cancer-cell-induced EMT and metastasis.

cancer biology↗

bioRxiv2023

Hypermetabolic state is associated with circadian rhythm disruption in mouse and human cancer cells

Crosstalk between cellular metabolism and circadian rhythms is a fundamental building block of multicellular life, and disruption of this reciprocal communication could be relevant to degenerative disease, including cancer. Here, we investigated whether maintenance of circadian rhythms depends upon specific metabolic pathways, particularly in the context of cancer. We found that in adult mouse fibroblasts, ATP levels were a major contributor to overall levels of a clock gene luciferase reporter, although not necessarily to the strength of circadian cycling. In contrast, we identified significant metabolic control of circadian function in an in vitro mouse model of pancreatic adenocarcinoma. Metabolic profiling of a library of congenic tumor cell clones revealed significant differences in levels of lactate, pyruvate, ATP, and other crucial metabolites that we used to identify candidate clones with which to generate circadian reporter lines. Despite the shared genetic background of the clones, we observed diverse circadian profiles among these lines that varied with their metabolic phenotype: the most hypometabolic line had the strongest circadian rhythms while the most hypermetabolic line had the weakest rhythms. Treatment of these tumor cell lines with bezafibrate, a peroxisome proliferator-activated receptor (PPAR) agonist shown to increase OxPhos, decreased the amplitude of circadian oscillation in a subset of tumor cell lines. Strikingly, treatment with the Complex I antagonist rotenone enhanced circadian rhythms only in the tumor cell line in which glycolysis was also low, thereby establishing a hypometabolic state. We further analyzed metabolic and circadian phenotypes across a panel of human patient-derived melanoma cell lines and observed a significant negative association between metabolic activity and circadian cycling strength. Together, these findings suggest that metabolic heterogeneity in cancer directly contributes to circadian function, and that high levels of glycolysis or OxPhos independently disrupt circadian rhythms in these cells.

cancer biology↗

bioRxiv2023

Physiological reprogramming in vivo mediated by Sox4 pioneer factor activity

Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cells enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.

cell biology↗

bioRxiv2022

p53 restoration in small cell lung cancer identifies a latent Cyclophilin-dependent necrosis mechanism

The p53 tumor suppressor regulates multiple context-dependent tumor suppressive programs. Although p53 is mutated in [~]90% of small cell lung cancer (SCLC) tumors, how p53 mediates tumor suppression in this context is unknown. Here, using a mouse model of SCLC in which endogenous p53 expression can be conditionally and temporally regulated, we show that SCLC tumors maintain a requirement for p53 inactivation. However, we identified tumor subtype heterogeneity between SCLC tumors such that p53 reactivation induces a canonical senescence response in a subset of tumors, while, in others, p53 induces a non-apoptotic form of cell death that culminates in necrosis. We pinpointed the cyclophilin family of peptidyl prolyl cis-trans isomerases as critical determinants of a p53-induced transcriptional program that is specific to SCLC tumors and cell lines that are poised to undergo p53-mediated necrosis. Importantly, inhibition of cyclophilin isomerase activity suppresses SCLC subtype-specific p53-mediated death by limiting p53 transcriptional output without impacting chromatin binding. Our study demonstrates that intertumoral heterogeneity in SCLC can influence the biological response to p53 restoration, describes a novel mechanism of p53-regulated necrotic cell death, and uncovers new targets for the treatment of this most-recalcitrant tumor type.

cancer biology↗

bioRxiv2022

Rapid in vivo multiplexed editing (RIME) of the adult mouse liver

Background & AimsAssessing mammalian gene function in vivo has traditionally relied on manipulation of the mouse genome in embryonic stem cells or peri-zygotic embryos. These approaches are time consuming and require extensive breeding when simultaneous mutations in multiple genes is desired. The aim of this study is to introduce a Rapid In vivo Multiplexed Editing (RIME), and to provide a proof-of-concept of this system. Approach & ResultsRIME, a system wherein CRISPR/Cas9 technology, paired with adeno-associated viruses (AAVs), permits the inactivation of one or more genes in the adult mouse liver. The method is quick, requiring as little as 1 month from conceptualization to knockout (KO), and highly efficient, enabling editing in >95% of target cells. To highlight its utility, we used this system to inactivate, alone or in combination, genes with functions spanning metabolism, mitosis, mitochondrial maintenance, and cell proliferation. ConclusionRIME enables the rapid, efficient, and inexpensive analysis of multiple genes in the mouse liver in vivo.

physiology↗

bioRxiv2021

MYC controls metastatic heterogeneity in pancreatic cancer

The degree of metastatic disease varies widely amongst cancer patients and impacts clinical outcomes. However, the biological and functional differences that drive the extent of metastasis are poorly understood. We analyzed primary tumors and paired metastases using a multi-fluorescent lineage-labeled mouse model of pancreatic ductal adenocarcinoma (PDAC) - a tumor type where most patients present with metastases. Genomic and transcriptomic analysis revealed an association between metastatic burden and gene amplification or transcriptional upregulation of MYC and its downstream targets. Functional experiments showed that MYC promotes metastasis by recruiting tumor associated macrophages (TAMs), leading to greater bloodstream intravasation. Consistent with these findings, metastatic progression in human PDAC was associated with activation of MYC signaling pathways and enrichment for MYC amplifications specifically in metastatic patients. Collectively, these results implicate MYC activity as a major determinant of metastatic burden in advanced PDAC.

cancer biology↗

bioRxiv2020

Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation

Cancer patients presenting with surgically resectable disease often harbor occult metastases, a potential source of relapse that is targetable only through systemic therapy. Studies of this occult fraction have been limited by a lack of tools with which to isolate discrete cells based on spatial grounds. We developed PIC-IT, photoconversion-based isolation technique allowing efficient recovery of cell clusters of any size including solitary disseminated tumor cells (DTCs), which are largely inaccessible otherwise. In a murine pancreatic cancer model, transcriptional profiling of spontaneously arising DTCs revealed phenotypic heterogeneity, functionally reduced propensity to proliferate and enrichment for inflammatory-response phenotype associated with NF-{kappa}B /AP-1 signaling. Pharmacological inhibition of NF-{kappa}B depleted DTCs but had no effect on macrometastases, suggesting DTCs are particularly dependent on this pathway. PIC-IT enables systematic investigation of the earliest stages of metastatic colonization. Moreover, this new technique can be applied to other biological systems in which isolation and characterization of spatially distinct cell populations is not currently feasible.

cancer biology↗

bioRxiv2018

Pharmacologic activation of G protein-coupled estrogen receptor inhibits pancreatic ductal adenocarcinoma

Female sex is associated with lower incidence and improved clinical outcomes for many cancer types, including pancreatic ductal adenocarcinoma (PDAC). Although the mechanisms responsible for this sex difference are unknown, recent data suggests nonclassical estrogen signaling through the G Protein-coupled Estrogen Receptor (GPER) is likely involved. Here we used murine syngeneic tumor models and human xenografts to test whether GPER signaling inhibits pancreatic ductal adenocarcinoma (PDAC). Activation of GPER with the specific, small molecule agonist G-1 inhibited PDAC proliferation, depleted c-Myc and programmed death ligand 1 (PD-L1), and increased tumor cell immunogenicity. Systemically delivered G-1 was well tolerated in PDAC bearing mice, significantly prolonged survival, and markedly increased the efficacy of PD-1 targeted immune therapy. We detected GPER protein in a majority of spontaneous human PDAC tumors. These data, coupled with the wide tissue distribution of GPER, and our previous work showing that G-1 inhibits melanoma, suggest that GPER agonists may be useful against many different cancer types.

cancer biology↗