Biology subjects

McAllister, F.

Publications and source records attributed to McAllister, F..

12 recordsLinked to original sources

bioRxiv2026

Oncogenic KRAS-MAPK signaling sustains a CD73 dependent therapeutic vulnerability in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is predominantly driven by oncogenic KRAS signaling and sustained by a desmoplastic, immunosuppressive microenvironment limiting therapeutic response. CD73 mediated adenosine signaling supports this immune-excluded, tumor supportive microenvironment. Whether dual targeting of KRAS-MAPK and CD73 signaling creates a therapeutic opportunity to improve tumor control remains unexplored. Analysis of KRAS mutant cancer cell lines revealed increased expression of NT5E and adenosine receptor ADORA2B. Pharmacologic and genetic suppression of oncogenic KRAS inhibited CD73 expression through a MAPK-dependent program. In syngeneic KPC tumors, conversely, CD73 inhibition with quemliclustat increased ERK phosphorylation in vivo, suggesting adaptive MAPK activation following CD73 blockade. Combined CD73 and RAS(ON) inhibition in vivo produced the strongest antitumor response, reducing endpoint tumor volume beyond either monotherapy. This combination significantly suppressed tumor proliferation and SMA-positive stroma and resulted in a substantial reduction in CD163-positive macrophage infiltration. RAS-MAPK targeted therapy was also associated with increased CD8-positive T cell infiltration and granzyme B-positive staining. As therapeutic responses in PDAC have been linked to the gut microbiome, we further examined treatment-associated changes in the microbiome. RAS-MAPK inhibition produced the most pronounced microbial alterations, which correlated with tumor volume and immune markers. Together, these findings identify KRAS-MAPK driven CD73 signaling as a therapeutic vulnerability in PDAC and support combined CD73 and RAS(ON) inhibition as a strategy to suppress tumor growth, remodel stroma, and alleviate tumor-associated immune suppression.

cancer biology↗

bioRxiv2026

KRAS-driven metabolic reprogramming of enhanced MFSD2A-mediated lysophosphatidylcholine scavenging promotes survival and progression of pancreatic ductal adenocarcinoma

Oncogenic KRAS drives lipid reprogramming in pancreatic ductal adenocarcinoma (PDAC) to promote disease progression, and these changes are manifest in circulation. Using mass spectrometry, we performed lipidomic analyses on plasmas from a cohort of 93 newly-diagnosed resectable PDAC cases, 43 patients with chronic pancreatitis, and 93 age- and sex-matched healthy controls, the results of which revealed pronounced reductions in circulating lysophosphatidylcholines (LysoPC) as a prominent feature associated with PDAC. Using stable-isotope resolved lipidomics, we further found that PDAC cells exhibit a lipid scavenging phenotype characterized by preferential uptake of extracellular unsaturated LysoPCs to sustain pro-growth signals. Restricting bioavailability of extracellular unsaturated LysoPCs shifted the metabolic phenotype of PDAC cells towards enhanced de novo lipogenesis and autophagy, which was accompanied by suppression of AKT signaling activities and increased susceptibility to apoptosis. Using bulk, single-cell, and spatial transcriptomic datasets together with functional experiments, we identified oncogenic KRAS-mediated upregulation of major facilitator superfamily domain-containing protein 2a (MFSD2A) as a key mediator that facilitates extracellular uptake of LysoPCs in PDAC cells. Loss of MFSD2A expression mimicked LysoPC restriction and resulted in inhibition of AKT signaling and increased propensity of PDAC cells to undergo apoptosis in vitro and suppressed tumor growth in vivo. Therapeutic targeting of the KRAS-MFSD2A-LysoPC axis via repurposing of the synthetic alkyl-lysophospholipid edelfosine promoted potent anti-cancer effects in vitro that were mechanistically attributed to reduced extracellular uptake of LysoPCs, and attenuation of AKT signaling. Collectively, our findings describe a previously unrecognized onco-metabolic program of enhanced LysoPC scavenging mediated by MFSD2A that promotes PDAC progression and that is therapeutically targetable via repurposing edelfosine.

cancer biology↗

bioRxiv2026

PTPN1/2 inhibits alveolar macrophage-mediated control of lung metastasis

Metastasis remains the leading cause of cancer mortality, yet effective therapies are limited. While therapeutic responses are influenced by organ-specific immune microenvironments, strategies to pharmacologically modulate these niches remain poorly defined. Here, using the clinical-stage inhibitor ABBV-CLS-484 (AC484) as a chemical probe, we demonstrate that systemic PTPN1/2 inhibition remodels the pulmonary myeloid landscape, specifically activating alveolar macrophages (AMs) toward a tumoricidal state. Integrated single-cell/spatial transcriptomics and functional assays reveal that AC484 promotes AM accumulation within metastatic lesions, elevates their IFN{gamma} production and responsiveness, and enhances their tumor-killing activity. Depletion of AMs diminishes the anti-metastatic efficacy of AC484. Mechanistically, inhibiting PTPN1/2 by AC484 amplifies IFN{gamma}-STAT1 signaling in AMs, while disrupting this pathway impairs their tumor control capability. These findings delineate a distinct innate immune axis where PTPN1/2 acts as a molecular "brake" on AM activation, suggesting that pharmacologically unleashing tissue-resident macrophages offers a therapeutic strategy to overcome metastatic progression, particularly in microenvironments where adaptive immunity is insufficient. SignificanceAMs are potent anti-metastatic immune effectors functionally constrained by PTPN1/2. Pharmacologically inhibiting PTPN1/2 amplifies their IFN{gamma}-STAT1 signaling and tumoricidal activity, establishing a strategy to reactivate tissue-resident immunity against metastasis.

immunology↗

bioRxiv2025

Dietary Fat Content Influences PanIN Progression and Pancreatic Cancer Development in Mice

Dietary macronutrient composition has emerged as a key modulator of pancreatic tumorigenesis, yet the impact of lipid-rich diets, particularly ketogenic diets (KD) on the earliest stages of pancreatic cancer development remains unclear. To investigate how dietary lipids shape the initiation and progression of Kras-driven neoplasia, we examined the effects of low-fat diet (LFD), high-fat diet (HFD), and KD in the Ptf1aCreERT2;KrasG12V (AcinarKrasG12V) mouse model. KD-fed mice showed the shortest survival (median 26 {+/-} 7 days) compared with SD (87 {+/-} 29; p = 0.02) and LFD (57 {+/-} 27; p = 0.02), while HFD-fed mice also exhibited reduced survival relative to SD (35 {+/-} 25; p = 0.05). KD feeding induced severe glucose intolerance and elevated circulating {beta}-hydroxybutyrate levels. Histologically, KD-fed AcinarKrasG12V mice developed invasive, sarcomatoid-like pancreatic ductal adenocarcinoma (PDAC), while HFD-fed mice showed increased poorly differentiated PDAC; in both groups these aggressive tumors were associated with extensive fibrosis and increased stromal CD39 expression relative to tumor compartments. Proteomic analysis demonstrated activation of PI3K-Akt-mTOR and EGFR signaling in KD and HFD-fed AcinarKrasG12V mice. Serum cytokines/chemokines profiling revealed pro-inflammatory and pro-angiogenic milieu in KD-fed AcinarKrasG12Vmice. Collectively, these results show that dietary lipid enrichment prior to oncogenic Kras activation may accelerate early pancreatic neoplasia and foster a microenvironment conducive to tumor progression. These findings underscore the need for careful consideration of KD use in individuals at elevated risk for pancreatic cancer.

cancer biology↗

bioRxiv2025

Platform-dependent effects of genetic variants on plasma APOL1 and their implications for kidney disease

Mutations in apolipoprotein L1 (APOL1) are strongly associated with protection against parasitic infections and increased risk of kidney disease in individuals of African ancestry. To better understand the mechanisms underlying APOL1-related pathologies, we examined genetic drivers of circulating APOL1 in individuals of African and European ancestry from four independent cohorts (UK Biobank, AASK, deCODE, and Health ABC) using three proteomic technologies (Olink, SomaLogic, and mass spectrometry). We found that disease-associated APOL1 G1 and G2 variants are strong cis-pQTLs for plasma APOL1 measured by Olink and SomaLogic, but not mass spectrometry. Critically, the direction of variant effects differed between proteomic platforms, being positive with Olink and negative with SomaLogic. We identified an additional APOL1 missense variant (rs2239785), common in Europeans, exhibiting the same platform-dependent directional discrepancy. Furthermore, variants in the kallikrein-kinin system (KKS), involving KLKB1, F12, and KNG1, and their genetic interactions showed strong trans-pQTL effects on APOL1 measured by Olink, but not SomaLogic. These platform-dependent discrepancies raise the possibility that both intrinsic APOL1 mutations and extrinsic KKS activity induce conformational changes in the APOL1 protein that are differentially recognized by the proteomic platforms.

genetics↗

bioRxiv2024

Aerobic exercise promotes PDAC vascular normalization through S1PR1 signaling in tumor endothelial cells

Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by high resistance to anti-cancer therapies. This resistance is caused in part by hypo-vascularization and dysfunctional vessels which inefficiently deliver chemotherapy. Here, we define the mechanism of aerobic exercise-induced tumor vascular remodeling and improved chemotherapy delivery and efficacy. We found that aerobic exercise was able to improve tumor vascular function and increase the number of lymphatic vessels, and these effects were associated with increased gemcitabine delivery to and efficacy against PDAC in mice. Further, exercise increased sphingosine-1-phosphate (S1P) in plasma and the activation of sphingosine-1-phosphate receptor 1 (S1PR1) in tumor endothelial cells. S1PR1 endothelial cell-specific deletion blunted the exercise-induced improvements in tumor vascular function, gemcitabine efficacy and drug concentration. Preclinical findings were validated in a patient cohort in which we found that exercise during neoadjuvant chemotherapy remodeled PDAC vasculature and improved tumor vascular function. These findings provide direct evidence that exercise increases chemotherapy delivery and efficacy by improving vascular function, defining S1PR1 as a necessary mediator of exercise-induced vascular remodeling.

cancer biology↗

bioRxiv2023

Host-microbe interactions mediate doramectin-promoted metabolic reprogramming of CD8+ T-cells and amplify antitumor immunity

The intestinal microbiota and its metabolites influence the host metabolic environment and CD8+ T-cell function. Metabolic changes in T-cells are thought to enhance the antitumor immune response. Here, we show that doramectin (DOR), a macrocyclic lactone (ML) of the avermectin (AVM) family, can modify CD8+ T-cell metabolism to increase and accelerate effector function. However, the functional capability of DOR depends mainly on the accessibility of gut microbiota. Using metagenomic and metabolomic techniques, we describe for the first time the interplay between gut microbiota and host metabolism involved in metabolic reprogramming of CD8+-T cells following DOR administration. Interestingly, we found that, after DOR administration, Firmicutes phylum not only impact DOR transport and absorption, but also boost amino acid levels in CD8+ T-cells, consistent with increased production of tumor necrosis factor alpha (TNF-) and, in particular, interferon gamma (IFN-{gamma}), which together play an important role in antitumor immunity. In contrast, the dysbiotic microbial community may abrogate the anticancer efficacy of DOR and lead to enhanced tumor growth and decreased survival. This finding likely supports the view that the presence of certain bacteria in the gut governs extra-intestinal immune responses and may be associated with metabolic adaptations necessary for efficient function of CD8+ T-cells upon DOR administration.

cancer biology↗

bioRxiv2021

Pancreatic cancer ductal cell of origin drives CD73-dependent generation of immunosuppressive adenosine

The microenvironment that surrounds pancreatic ductal adenocarcinoma (PDAC) is profoundly desmoplastic and immunosuppressive. Understanding initial triggers of immunosuppression during the process of pancreatic tumorigenesis would aid in establishing novel targets for effective prevention and therapy. Here, we interrogate the differential molecular mechanisms dependent on cell of origin and pathology subtype that determine immunosuppression during PDAC initiation and in established tumors. Transcriptomic analysis of cell of origin dependent-epithelial gene signatures revealed that Nt5e/CD73, a cell surface enzyme that is the pacemaker for extracellular adenosine generation, is one of the top 10% of genes over-expressed in murine tumors arising from ductal pancreatic epithelium as opposed to those rising from acinar cells. These findings were confirmed by Imaging Mass Cytometry and High-Performance Liquid Chromatography. Our data indicate that ductal activation of oncogenic mutant Kras results in loss of PTEN and elevated AKT signaling which ultimately releases CD73 suppression. Delivery of CD73 small molecule inhibitors through various delivery routes reduced tumor development and growth in genetically engineered and syngeneic mouse models. Analysis in human PDAC subtypes indicates that high Nt5e in murine ductal PDAC models overlaps with high NT5E in human PDAC Squamous and Basal Subtypes, considered to have the highest immunosuppression and worst prognosis. These findings highlight a molecular trigger of the immunosuppressive PDAC microenvironment which is dependent on ductal cell of origin, linking biology with pathological subtype classification, critical components to personalized approaches for PDAC prevention and immunotherapeutic intervention. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/470415v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@14625org.highwire.dtl.DTLVardef@1a43372org.highwire.dtl.DTLVardef@12dc0c8org.highwire.dtl.DTLVardef@cbb835_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Adar1 deletion causes degeneration of exocrine pancreas via Mavs-dependent interferon signaling

Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-binding protein that deaminates adenosine(A) to inosine(I). A-to-I editing alters post-transcriptional RNA processing making ADAR1 a critical regulator of gene expression. Consequently, Adar1 has been implicated in organogenesis. To determine the role of Adar1 in pancreatic development and homeostasis, we specifically deleted Adar1 from the murine pancreas (Ptf1aCre/+; Adar1Fl/Fl). The resulting mice had stunted growth likely due to malabsorption associated with exocrine pancreas insufficiency. Analyses of pancreases revealed ductal expansion, heightened interferon-stimulated gene expression and an increased influx of immune cells. In addition, we observed an increased prevalence of CD4+ T and natural killer cells in their splenic tissue. These results indicate an association between loss of pancreatic Adar1 with dysregulation of systemic immunity. Concurrent deletion of Adar1 and Mavs, a signaling protein implicated in the innate immune pathway rescued the degenerative phenotype and resulted in normal pancreatic development. Taken together, our work suggests that the primary function of Adar1 in the pancreas is to prevent aberrant activation of the Mavs-mediated innate immune pathway, thereby maintaining pancreatic homeostasis. Summary statementThis work defines the role of Adar1 in pancreatic development and homeostasis.

developmental biology↗

bioRxiv2021

Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin

The process wherein dividing cells exhaust proliferative capacity and enter into replicative senescence has become a prominent model for cellular aging in vitro. Despite decades of study, this cellular state is not fully understood in culture and even much less so during aging. Here, we revisit Leonard Hayflicks original observation of replicative senescence in WI-38 human lung fibroblasts equipped with a battery of modern techniques including RNA-seq, single cell RNA-seq, proteomics, metabolomics, and ATAC-seq. We find evidence that the transition to a senescent state manifests early, increases gradually, and corresponds to a concomitant global increase in DNA accessibility in nucleolar and lamin associated domains. Furthermore, we demonstrate that senescent WI-38 cells acquire a striking resemblance to myofibroblasts in a process similar to the epithelial to mesenchymal transition (EMT) that is regulated by the transcription factors YAP1/TEAD1 and TGF-{beta}2. Lastly, we show that verteporfin inhibition of YAP1/TEAD1 activity in aged WI-38 cells robustly attenuates this gene expression program.

genomics↗

bioRxiv2020

Precise Estimation of In Vivo Protein Turnover Rates

Isotopic labeling with deuterium oxide (D2O) is a common technique for estimating in vivo protein turnover, but its use has been limited by two long-standing problems: (1) identifying non-monoisotopic peptides; and (2) estimating protein turnover rates in the presence of dynamic amino acid enrichment. In this paper, we present a novel experimental and analytical framework for solving these two problems. Peptides with high probabilities of labeling in many amino acids present fragmentation spectra that frequently do not match the theoretical spectra used in standard identification algorithms. We resolve this difficulty using a modified search algorithm we call Conditional Ion Distribution Search (CIDS). Increased identifications from CIDS along with direct measurement of amino acid enrichment and statistical modeling that accounts for heterogeneous information across peptides, dramatically improves the accuracy and precision of half-life estimates. We benchmark the approach in cells, where near-complete labeling is possible, and conduct an in vivo experiment revealing, for the first time, differences in protein turnover between mice and naked mole-rats commensurate with their disparate longevity.

bioinformatics↗

bioRxiv2018

Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model

PurposeThe lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated to the abysmal survival rate in patients. In addition to several potential detection tools under active investigation, we tested the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high-risk for PDAC.\n\nExperimental DesignA combination of 16s pyrosequencing and whole-genome sequencing of gut microbiota was used in a spontaneous genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC). Metabolic reconstruction of microbiome was done using the HUmanN2 pipeline. Serum polyamine levels were measured from murine and patient samples using standard methods.\n\nResultsResults showed a progressive Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentration. Therefore, at the early stages of tumorigenesis, the gut microbial composition changes in a way to release metabolites that foster host tumorigenesis, thereby fulfilling the vicious cycle hypothesis of the role of the microbiome in health and disease states.\n\nConclusionsOur results provide a potential, precise, non-invasive tool for early detection of PDAC, which will result in improved outcomes.\n\nSynopsisGut microbiota changes during early stages of pancreatic ductal adenocarcinoma (PDAC) progression and contributes towards host polyamine pool. Both changes can be used as an early predictive marker for PDAC.\n\nTranslational RelevancePancreatic carcinogenesis progresses through pre-cancerous PanIN lesions to invasive cancer. Even though these morphological changes are histologically distinct, imaging techniques are not able to distinguish the pre-invasive PanINs from normal pancreas, making detection of a tumor at a precancerous stage impossible. Thus, majority of cases (85-90%) present with advanced pancreatic cancer at the time of diagnosis. This contributes to the dismal survival rate in this disease. Our study of gut microbiome analysis on KPC mice during tumor progression followed by metabolic reconstruction and experimental validation in human samples indicate that gut-microbiome analysis along with an analysis of the microbial metabolites can be developed as potential biomarkers for detection of PDAC at early stages when histological changes are not yet grossly apparent.

cancer biology↗