Biology subjects

MacKeigan, J. P.

Publications and source records attributed to MacKeigan, J. P..

4 recordsLinked to original sources

bioRxiv2026

ULK1 drives NDP52-mediated selective autophagic degradation of MHC-I to promote immune evasion in HPV-positive head and neck cancer

Antigen presentation by major histocompatibility complex class I (MHC-I) is critical for tumor cell killing by CD8+ T cells. Accordingly, tumor cells downregulate MHC-I expression through multiple mechanisms, thereby evading the immune response. Importantly, lower levels of MHC-I are associated with poor responses to immune checkpoint inhibitor therapy. Our recent study has shown that the human papillomavirus (HPV) oncoproteins induce MHC-I protein ubiquitination by membrane-associated Ring-CH-type finger 8 (MARCHF8) in HPV-positive head and neck cancer (HPV+ HNC). However, the mechanism by which ubiquitinated MHC-I is degraded remains elusive. By performing genome-wide CRISPR screens, we identified components of the ULK1 and PIK3C3 complexes for autophagy initiation complexes among the top negative regulators of cell-surface MHC-I expression in HPV+ HNC cells. We show that MHC-I is recruited from the ER to autophagosomes by the cargo receptor NDP52, decreasing MHC-I levels. Further, inhibiting the initiation or nucleation steps of autophagy before autophagosome formation is critical for restoring MHC-I levels on the cell surface. Finally, genetic inhibition of autophagy initiation suppresses HPV+ HNC tumor growth in vivo and enhances the CD8+ T cell-mediated antitumor response. Our findings suggest that autophagic degradation of MARCHF8-ubiquitinated MHC-I is a key immune evasion mechanism in HPV+ HNC.

cancer biology↗

bioRxiv2023

Quantitative Analysis of Autophagy in Single Cells: Differential Response to Amino Acid and Glucose Starvation

Autophagy is a highly conserved, intracellular recycling process by which cytoplasmic contents are degraded in the lysosome. This process occurs at a low level constitutively; however, it is induced robustly in response to stressors, in particular, starvation of critical nutrients such as amino acids and glucose. That said, the relative contribution of these inputs is ambiguous and many starvation medias are poorly defined or devoid of multiple nutrients. Here, we sought to generate a quantitative catalog of autophagy across multiple stages and in single, living cells under normal growth conditions as well as in media starved specifically of amino acids or glucose. We found that autophagy is induced by starvation of amino acids, but not glucose, in U2OS cells, and that MTORC1-mediated ULK1 regulation and autophagy are tightly linked to amino acid levels. While autophagy is engaged immediately during amino acid starvation, a heightened response occurs during a period marked by transcriptional upregulation of autophagy genes during sustained starvation. Finally, we demonstrated that cells immediately return to their initial, low-autophagy state when nutrients are restored, highlighting the dynamic relationship between autophagy and environmental conditions. In addition to sharing our findings here, we provide our data as a high-quality resource for others interested in mathematical modeling or otherwise exploring autophagy in individual cells across a population.

cell biology↗

bioRxiv2018

Tissue distribution and tumor concentrations of hydroxychloroquine and quinacrine analogs in mice

Hydroxychloroquine (HCQ) is a 4-aminoquinoline molecule used for the treatment of malaria, and more recently to treat rheumatoid arthritis, systemic lupus erythematosus, and cancer. In cancer, HCQ is being used in multiple cancer clinical trials as an inhibitor of autophagy, a cytosolic degradation process employing the lysosome. Importantly, more potent lysosomotropic agents are being developed as autophagy inhibitors. Additional studies revealed that acridine-based compounds such as quinacrine (QN) increased potency over the 4-aminoquinoline HCQ. In line with these initial discoveries, we performed chemical synthesis of acridine-based compounds and screened for potent autophagy inhibition. The novel compound VATG-027 increased potency and cytotoxicity over HCQ in osteosarcoma and melanoma cell lines, supporting further investigation in vivo. Here, we developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) method to investigate HCQ, QN, and VATG-027 compound concentrations across various tissue types in mice. This method detected compound concentrations in whole blood, lung, liver, kidney, and subcutaneous tumor tissues. Concentrations of HCQ, QN, and VATG-027 varied within and between tissue types, suggesting unique tissue distribution profiles for 4-aminoquinoline and acridine compounds.

pharmacology and toxicology↗

bioRxiv2017

DDK has a primary role in processing stalled replication forks to initiate downstream checkpoint signaling

CDC7-DBF4 kinase (DDK) is required to initiate DNA replication in eukaryotes by activating the replicative MCM helicase. DDK has also been reported to have diverse and sometimes conflicting roles in the replication checkpoint response in various organisms but the underlying mechanisms are far from settled. Here we show that human DDK promotes limited resection of newly synthesized DNA at stalled replication forks or sites of DNA damage to initiate replication checkpoint signaling. DDK is also required for efficient fork restart and G2/M cell cycle arrest. DDK exhibits genetic interactions with the ssDNA exonuclease EXO1, and we show that EXO1 is also required for nascent strand degradation following exposure to HU, raising the possibility that DDK regulates EXO1 directly. Thus, DDK has a primary and previously undescribed role in the replication checkpoint to promote ssDNA accumulation at stalled forks, which is required to initiate a robust checkpoint response and cell cycle arrest to maintain genome integrity.

cell biology↗