Biology subjects

Macleod, K. F.

Publications and source records attributed to Macleod, K. F..

7 recordsLinked to original sources

bioRxiv2026

DHHC7 palmitoylates KRAS4A and promotes mutant KRAS-driven pancreatic cancers

KRAS mutations underlie many human cancers. While inhibitors such as Sotorasib and Adagrasib targeting KRAS mutants have shown promise, additional strategies are required to address the broader spectrum of KRAS-driven cancers, particularly those displaying drug resistance. Thus, there is a need to better understand KRAS signaling and develop new therapeutic strategies. Here we show that KRAS4A is palmitoylated on Cys180 by a palmitoyl transferase, DHHC7 (gene name ZDHHC7). Palmitoylation promotes KRAS4A plasma membrane localization, and more importantly, nanoclustering. This in turn promotes the activation of ARAF and RAF1, but not BRAF. DHHC7 and KRAS4A Cys180 palmitoylation are important for the normal and anchorage independent growth of pancreatic cancer cell lines. Depletion of ZDHHC7 dramatically inhibits pancreatic tumor growth in mouse xenograft models. These studies provide new understandings about how palmitoylation regulates KRAS4A activity and suggest DHHC7 as a promising new target for KRAS mutant cancers.

cancer biology↗

bioRxiv2025

Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer

Systemic therapies are the standard of care for most pancreatic ductal adenocarcinoma (PDAC) patients but provide limited benefit due to pervasive resistance. The fibrotic tumor microenvironment (TME) is thought to drive resistance by restricting perfusion and drug delivery. Here, we show that therapeutically relevant drug concentrations are achieved even in poorly perfused, therapy-resistant murine PDAC tumors, indicating that impaired delivery alone does not explain drug resistance. Instead, we find TME exposure imprints a therapy-resistant state upon PDAC cells. These observations raised the question of how the TME imposes this state. Poor perfusion alters nutrient availability in the TME. To model this, we developed Tumor Interstitial Fluid Medium (TIFM), which recapitulates TME nutrient conditions. TIFM cultured PDAC cells acquire a therapy-resistant phenotype that mirrors resistance observed in the TME. In this state, cytotoxic and targeted therapies retain on-target activity but fail to trigger cell death, resulting in therapeutic tolerance. Mechanistically, drug tolerance is driven by suppression of apoptotic priming and can be reversed by inhibition of the anti-apoptotic regulator BCL-XL. These results identify TME-driven reprogramming of cell death as a key mechanism of therapy resistance in PDAC and establish TIFM as a physiologically relevant model for studying microenvironment-induced drug resistance.

cancer biology↗

bioRxiv2025

Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis

Nutrient limitation is a characteristic feature of poorly perfused tumors. In contrast to well-perfused tissues, nutrient deficits in tumors impose metabolic constraints on cancer cells. The metabolic constraints created by the tumor microenvironment can lead to vulnerabilities in cancers. Identifying the metabolic constraints of the tumor microenvironment and the vulnerabilities that arise in cancers can provide new insight into tumor biology and identify promising antineoplastic targets. To identify how the microenvironment constrains the metabolism of pancreatic tumors, we challenged pancreatic cancer cells with microenvironmental nutrient levels and analyzed changes in cellular metabolism. We found that arginine limitation in pancreatic tumors perturbs saturated and monounsaturated fatty acid synthesis by suppressing the lipogenic transcription factor SREBP1, in part via activation of the amino acid sensor GCN2. Synthesis of these fatty acids is critical for maintaining a balance of saturated, monounsaturated, and polyunsaturated fatty acids in cellular membranes. Because of microenvironmental constraints on fatty acid synthesis, pancreatic cancer cells and tumors are unable to maintain lipid homeostasis when exposed to polyunsaturated fatty acids, leading to cell death by ferroptosis. In sum, arginine restriction in the tumor microenvironment constrains lipid metabolism in pancreatic cancers, which renders these tumors vulnerable to polyunsaturated-enriched fats.

cancer biology↗

bioRxiv2024

Context-dependent roles for autophagy in myeloid cells in tumor progression

Autophagy is known to suppress tumor initiation by removing genotoxic stresses in normal cells. Conversely, autophagy is also known to support tumor progression by alleviating metabolic stresses in neoplastic cells. Centered on this pro-tumor role of autophagy, there have been many clinical trials to treat cancers through systemic blocking of autophagy. Such systemic inhibition affects both tumor cells and non-tumor cells, and the consequence of blocked autophagy in non-tumor cells in the context of tumor microenvironment is relatively understudied. Here, we examined the effect of autophagy-deficient myeloid cells on the progression of autophagy-competent tumors. We found that blocking autophagy only in myeloid cells modulated tumor progression markedly but such effects were context dependent. In a tumor implantation model, the growth of implanted tumor cells was substantially reduced in mice with autophagy-deficient myeloid cells; T cells infiltrated deeper into the tumors and were responsible for the reduced growth of the implanted tumor cells. In an oncogene-driven tumor induction model, however, tumors grew faster and metastasized more in mice with autophagy- deficient myeloid cells. These data demonstrate that the autophagy status of myeloid cells plays a critical role in tumor progression, promoting or suppressing tumor growth depending on the context of tumor-myeloid cell interactions. This study indicates that systemic use of autophagy inhibitors in cancer therapy may have differential effects on rates of tumor progression in patients due to effects on myeloid cells and that this warrants more targeted use of selective autophagy inhibitors in a cancer therapy in a clinical setting.

cancer biology↗

bioRxiv2023

Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition

Profiling tumors with single-cell RNA sequencing (scRNA-seq) has the potential to identify recurrent patterns of transcription variation related to cancer progression, and produce new therapeutically relevant insights. However, the presence of strong inter-tumor heterogeneity often obscures more subtle patterns that are shared across tumors, some of which may characterize clinically relevant disease subtypes. Here we introduce a new statistical method, generalized binary covariance decomposition (GBCD), to address this problem. We show that GBCD can help decompose transcriptional heterogeneity into interpretable components -- including patient-specific, dataset-specific and shared components relevant to disease subtypes -- and that, in the presence of strong inter-tumor heterogeneity, it can produce more interpretable results than existing methods. Applied to data from three studies on pancreatic cancer adenocarcinoma (PDAC), GBCD produces a refined characterization of existing tumor subtypes (e.g., classical vs. basal), and identifies a new gene expression program (GEP) that is prognostic of poor survival independent of established prognostic factors such as tumor stage and subtype. The new GEP is enriched for genes involved in a variety of stress responses, and suggests a potentially important role for the integrated stress response in PDAC development and prognosis.

genomics↗

bioRxiv2022

Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress

Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs to maintain survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (Sullivan et al., 2019a). Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling study of PDAC metabolism under physiological nutrition. We show that PDAC cells cultured in TIFM, compared to standard laboratory models, adopt a cellular state more similar to PDAC cells in tumors. Further, using the TIFM model we identified arginine biosynthesis as a metabolic adaptation PDAC cells engage to cope with microenvironmental arginine starvation driven by myeloid cells in PDAC tumors. Altogether, these data show that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity and enable the discovery of novel cancer metabolic phenotypes.

cancer biology↗

bioRxiv2017

Formin-Dependent Adhesions Are Required For Invasion By Epithelial Tissues

Developing tissues change shape, and tumors initiate spreading, through collective cell motility. Conserved mechanisms by which tissues initiate motility into their surroundings are not known. We investigated cytoskeletal regulators during collective invasion by mouse tumor organoids and epithelial MDCK acini undergoing branching morphogenesis. Inhibition of formins, but not Arp2/3, prevented the formation of migrating cell fronts in both cell types. MDCK cells depleted of the formin protein Dia1 formed polarized acini and could execute planar cell motility, either within the acinus or in 2D scattering assays. However, Dia1 was required to form protrusions into the collagen matrix. Live imaging of actin, myosin, and collagen in control acini revealed adhesions that deformed individual collagen fibrils, while Dia1-depleted acini exhibited unstable adhesions with minimal collagen deformation. This work identifies Dia1-mediated adhesions as essential regulators of tissue shape changes, through their role in focal adhesion maturation.

cell biology↗