Biology subjects

Ilagan, M. X. G.

Publications and source records attributed to Ilagan, M. X. G..

5 recordsLinked to original sources

bioRxiv2025

ADAR1 Regulates Lipid Remodeling through MDM2 to Dictate Ferroptosis Sensitivity

Triple-negative breast cancer (TNBC), defined by the lack of estrogen, progesterone, and HER2 receptor expressions, is aggressive and lacks targeted treatment options. Adenosine deaminase acting on RNA 1 (ADAR1) has been shown to contribute to TNBC tumorigenesis by modulating an innate immune response. However, little is known about its role in the regulation of metabolic fitness of TNBC. We tested the hypothesis that ferroptosis is an ADAR1-protected vulnerability by showing that ADAR1 knockdown sensitizes TNBC cells to ferroptosis inducers. Lipidomic analyses showed that ADAR1 loss increased the abundance of phospholipids enriched with polyunsaturated fatty acids (PUFA), of which peroxidation is the main driver of ferroptosis. Transcriptomic analyses discovered that the proto-oncogene MDM2 contributes to the lipid remodeling phenotype. A ferroptosis-focused drug screen identified FDA-approved cobimetinib as a drug-repurposing candidate to synergize with ADAR1 loss. This finding supports further basic, pre-clinical, and clinical studies to develop novel therapeutic strategies for TNBC through ADAR1-mediated metabolic regulation.

cancer biology↗

bioRxiv2024

Cutibacterium adaptation to life on humans provides a novel biomarker of C. acnes infections.

The domestication of cattle provided Propionibacteriaceae the opportunity to adapt to human skin. These bacteria constitute a distinct genus (Cutibacterium), and a single species within that genus (C. acnes) dominates 25% of human skin. C. acnes protects humans from pathogen colonization, but it can also infect indwelling medical devices inserted through human skin. Proteins that help Cutibacteria live on our skin may also act as virulence factors during an opportunistic infection, like a shoulder periprosthetic joint infection (PJI). To better understand the evolution of this commensal and opportunistic pathogen, we sought to extensively characterize one of these proteins, RoxP. This secreted protein is only found in the Cutibacterium genus, helps C. acnes grow in oxic environments, and is required for C. acnes to colonize human skin. Structure-based sequence analysis of twenty-one RoxP orthologs (71-100% identity to C. acnes strain KPA171202 RoxP_1) revealed a high-degree of molecular surface conservation and helped identify a potential heme-binding interface. Biophysical evaluation of a subset of seven RoxP orthologs (71-100% identity) demonstrated that heme-binding is conserved. Computational modeling of these orthologs suggests that RoxP heme-binding is mediated by an invariant molecular surface composed of a surface-exposed tryptophan (W66), adjacent cationic pocket, and nearby potential heme axial ligands. Further, these orthologs were found to undergo heme-dependent oligomerization. To further probe the role of this protein in C. acnes biology, we developed four monoclonal anti-RoxP antibodies, assessed the binding of those antibodies to a subset of ten RoxP orthologs (71-100% identity), developed an anti-RoxP sandwich ELISA (sELISA) with sub-nanogram sensitivity, and adapted that sELISA to quantitate RoxP in human biofluids that can be infected by C. acnes (serum, synovial fluid, cerebrospinal fluid). This study expands our understanding of how an environmental bacterium evolved to live on humans, and the assays developed in this work can now be used to identify this organism when it gains access to sterile sites to cause opportunistic infections. Author SummaryThe longer humans live, the more they require internal "replacement parts," like prosthetic joints. Increased placement of these and other medical devices has increased their complications, which frequently are infections caused by microbes that live on humans. One of these microbes is Cutibacterium acnes, which dominates 25% of human skin. It appears that when humans domesticated cattle, a C. acnes ancestor adapted from living in cows to living on people. One of these adaptations was RoxP, a protein only found in Cutibacterium and carried by all C. acnes. Here, we describe our extensive characterization of RoxP. We found that distantly related RoxP conserve high stability at the low pH found on human skin. They also conserve the ability to bind heme, a source of iron used by microbes when they infect humans. As a part of this work, we developed tests that measure RoxP to identify C. acnes growth. In a clinic or hospital, these tests could allow a doctor to rapidly identify C. acnes infections, which would improve patient outcomes and lower healthcare costs. This work has helped us better understand how C. acnes adapted to live on humans and to identify C. acnes infections of medical devices.

microbiology↗

bioRxiv2020

Integrative omics data analysis uncovers biomarker genes and potential candidate drugs for G3 medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor in infants and children. Four molecular subtypes of MB are recognized: WNT, SHH, Group 3 (G3), and Group 4 (G4). Compared with WNT and SHH subtypes, G3 MBs exhibit significantly worse outcomes and higher metastatic rates, and there is no effective treatment yet. Moreover, G3 and G4 MBs are much more common in boys than girls, i.e., sex bias, which also plays important roles in cancer prognosis and drug response. However, the molecular mechanism of G3 remains unclear, and there are no well-identified biomarker genes associated with these phenotypes, i.e., worse survival rate, higher metastasis rate, and sex bias. In this exploratory study, we aim to identify potential biomarkers associated with the three phenotypes using integrative analysis of gene expression, methylation and copy number variation datasets. In the results, we identified a set of biomarker genes and linked them into a network signature. The network signature showed better performance in the separation of G3 MB patients into subtypes with a significant difference in terms of the three phenotypes. To identify potentially effective drugs for G3 MBs, a set of drugs with diverse targets were prioritized, which can potentially inhibit the network signature. These drugs or combinations thereof might be effective for G3 treatment.

bioinformatics↗

bioRxiv2020

Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.

Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly disrupt epidemic transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, yet there is no consensus as to which assay should be used for such measurements. Using an infectious molecular clone of vesicular stomatitis virus (VSV) that expresses eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. We compared the neutralizing activities of monoclonal and polyclonal antibody preparations, as well as ACE2-Fc soluble decoy protein in both assays and find an exceptionally high degree of concordance. The two assays will help define correlates of protection for antibody-based countermeasures including therapeutic antibodies, immune {gamma}-globulin or plasma preparations, and vaccines against SARS-CoV-2. Replication-competent VSV-eGFP-SARS-CoV-2 provides a rapid assay for testing inhibitors of SARS-CoV-2 mediated entry that can be performed in 7.5 hours under reduced biosafety containment.

microbiology↗

bioRxiv2019

The aminoalkylindole, BML-190, negatively regulates chitosan synthesis via the cAMP/PKA1 pathway in Cryptococcus neoformans

Cryptococcus neoformans can cause fatal meningoencephalitis in patients with AIDS or other immune-compromising conditions. Current antifungals are suboptimal to treat this disease, therefore, novel targets and new therapies are needed. Previously, we have shown that chitosan is a critical component of the cryptococcal cell wall, is required for survival in the mammalian host, and that chitosan deficiency results in rapid clearance from the mammalian host. We had also identified several specific proteins that were required for chitosan biosynthesis, and we hypothesize that screening for compounds that inhibit chitosan biosynthesis would identify additional genes/proteins that influence chitosan biosynthesis.\n\nTo identify these compounds we developed a robust and novel cell-based flow cytometry screening method to identify small molecule inhibitors of chitosan production. We screened the ICCB Known Bioactives library and identified 8 compounds that reduced chitosan in C. neoformans. We used flow cytometry-based counter and confirmatory screens, followed by a biochemical secondary screen to refine our primary screening hits to 2 confirmed hits.\n\nOne of the confirmed hits that reduced chitosan content was the aminoalkylindole, BML-190, a known inverse agonist of mammalian cannabinoid receptors. We demonstrated that BML-190 likely targets the C. neoformans G-protein coupled receptor, Gpr4, and via the cAMP/PKA signaling pathway, contributes to an intracellular accumulation of cAMP that results in decreased chitosan. Our discovery suggests that this approach could be used to identify additional compounds and pathways that reduce chitosan biosynthesis, and could lead to potential novel therapeutics against C. neoformans.\n\nImportanceCryptococcus neoformans is a fungal pathogen that kills [~]200,000 people every year. The cell wall is an essential organelle that protects fungus from the environment. Chitosan, the deacetylated form of chitin, has been shown to be an essential component of cryptococcal cells wall during infection of a mammalian host. In this study, we screened a set of 480 compounds, which are known to have defined biological activities, for activity that reduced chitosan production in C. neoformans. Two of these compounds were validated using an alternative method of measuring chitosan, and one of these was demonstrated to impact the cAMP signal transduction pathway. This work demonstrates that the cAMP pathway regulates chitosan in C. neoformans, and validates that this screening approach could be used to find potential antifungal agents.

microbiology↗