Biology subjects

Wilson, D. M.

Publications and source records attributed to Wilson, D. M..

8 recordsLinked to original sources

bioRxiv2026

Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1

Human AP-endonuclease 1 (APE1) is a vital enzyme in the base excision repair pathway that protects genome stability by eliminating ubiquitous abasic DNA lesions. Despite its importance and therapeutic potential, how APE1 achieves high specificity and single-metalion catalytic efficiency remains unclear. Here, we present a high-resolution structure of the APE1-DNA Michaelis complex coordinated with physiological cofactor Mg2+. Integrating this snapshot with ab initio molecular dynamics and metadynamics simulations reveals a novel "moving metal ion" mechanism in which Mg2+ undergoes orchestrated repositioning to trigger a concerted catalytic reaction, bypassing the formation of an associative pentavalent intermediate. This distinct catalytic strategy, driven by concerted active-site reorganization, enables APE1 to efficiently process damaged DNA using only one metal ion cofactor. A previously unrecognized hydrogen-bonding network couples catalytic water activation to the metal ion movement - two events that strikingly occur on opposite sides of the active site. These findings provide a blueprint for how enzymes synchronize distal active site rearrangements with transition state formation. Our results further suggest that effective AI-targeted inhibitor design should develop capacities to predict mechanistically critical non-canonical rotamers and transient hydrogen-bonding networks. Our combined findings offer a foundation for the design of inhibitors targeting APE1 overexpression in cancer.

biochemistry↗

bioRxiv2025

Effective imaging and treatment of Acute Myeloid Leukemia with radiotheranostics targeting the activated conformation of integrin-Beta2

There remains an unmet clinical need for improved treatment strategies in Acute Myeloid Leukemia (AML). Although radiopharmaceutical therapies targeting non-cancer-selective antigens have shown promise in AML, their clinical utility is often limited by prolonged bone marrow suppression. Using a unique proteomics-based strategy, we recently identified the active conformation of integrin-{beta}2 (aITGB2) as a novel, tumor-selective target for AML. Importantly, this conformational epitope is expressed widely on AML cells but minimally on normal marrow progenitors/healthy tissues. Here we first confirmed widespread aITGB2 expression on AML tumors that was largely independent of tumor genotype or prior therapeutic regimen. We developed diagnostic and therapeutic radiopharmaceuticals targeting aITGB2 utilizing a conformation-specific antibody (clone 7065). PET/CT imaging with 89Zr and 134Ce-labeled 7065 in AML models revealed high target-mediated uptake, greater than that compared to standard of care [18F]-FDG. PET/CT imaging with [89Zr]DFO*-7065 showed reduced binding to normal bone marrow and immune cells in humanized immune system mice compared to [89Zr]DFO*-anti-CD33. For therapy, we developed [225Ac]Macropa-PEG4-7065 using an optimized chelator-linker combination. Treatment with [225Ac]Macropa-PEG4-7065 in Nomo-1 and PDX AML disseminated models delayed tumor growth and improved overall survival compared to controls, including [225Ac]DOTA-anti-CD33, a clinical stage-radioimmunotherapy under evaluation in AML. Relapsed tumors demonstrated persistent aITGB2 expression, supporting continued development of fractionated dosing schemes, and proteomics analysis indicated activation of TCA cycle and carbon metabolism pathways, consistent with therapy-induced stress responses. These findings highlight [89Zr]DFO*-7065 and [225Ac]Macropa-7065 as a promising aITGB2-targeted theranostic pair with potential for imaging and treatment in future clinical translation. One Sentence SummaryThis study demonstrates promising preclinical efficacy of aITGB2-targeted radiotheranostics for selective imaging and therapy in AML.

cancer biology↗

bioRxiv2024

Molecular insights into the stimulation of SNM1A nuclease activity by CSB during interstrand crosslink processing

The Cockayne Syndrome B (CSB, ERCC6) protein, interacts with the exonuclease SNM1A during transcription-coupled DNA interstrand (ICL) repair, with CSB facilitating localisation of SNM1A to ICL damage. The functional and mechanistic details of this interaction in DNA repair, however, have not been defined. Here, we demonstrate that CSB enhances SNM1A resection through ICLs and identify a specific interaction between the winged-helix domain of CSB and the nuclease core of SNM1A that is crucial for recruitment and enhancement of nuclease degradation. Biochemical and single-molecule studies on DNA containing site-specific ICLs reveal that CSB increases the affinity of SNM1A to damaged DNA substrates and also alters the substrate conformation to enhance ICL processing by SNM1A. Notably, CSB was observed preferentially as a dimer when colocalised with SNM1A at ICLs, constrasting with its monomeric nature observed during repair initiation in classical transcription-coupled nucleotide excision repair. The combined results provide molecular insights into the basis of a direct contribution of CSB to a DNA repair reaction.

biochemistry↗

bioRxiv2023

Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from FDG yield potent sensors of living bacteria in vivo

Chemoenzymatic techniques have been applied extensively to pharmaceutical development, most effectively when routine synthetic methods fail. The regioselective and stereoselective construction of structurally complex glycans is an elegant application of this approach, that is seldom applied to positron emission tomography (PET) tracers. We sought a method to dimerize 2-deoxy-[18F]-fluoro-D-glucose ([18F]FDG), the most common tracer used in clinical imaging, to form [18F]-labeled disaccharides for detecting microorganisms in vivo based on their bacteria-specific glycan incorporation. When [18F]FDG was reacted with {beta}-D-glucose-1-phosphate in the presence of maltose phosphorylase, both the -1,4 and -1,3-linked products 2-deoxy-[18F]-fluoro-maltose ([18F]FDM) and 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK) were obtained. This method was further extended with the use of trehalose (,-1,1), laminaribiose ({beta}-1,3), and cellobiose ({beta}-1,4) phosphorylases to synthesize 2-deoxy-2-[18F]fluoro-trehalose ([18F]FDT), 2-deoxy-2-[18F]fluoro-laminaribiose ([18F]FDL), and 2-deoxy-2-[18F]fluoro-cellobiose ([18F]FDC). We subsequently tested [18F]FDM and [18F]FSK in vitro, showing accumulation by several clinically relevant pathogens including Staphylococcus aureus and Acinetobacter baumannii, and demonstrated their specific uptake in vivo. The lead sakebiose-derived tracer [18F]FSK was stable in human serum and showed high uptake in preclinical models of myositis and vertebral discitis-osteomyelitis. Both the synthetic ease, and high sensitivity of [18F]FSK to S. aureus including methicillin-resistant (MRSA) strains strongly justify clinical translation of this tracer to infected patients. Furthermore, this work suggests that chemoenzymatic radiosyntheses of complex [18F]FDG-derived oligomers will afford a wide array of PET radiotracers for infectious and oncologic applications.

microbiology↗

bioRxiv2023

Seedling performance in a dioecious tree species is similar near female and male conspecific adults despite differences in colonization by arbuscular mycorrhizal fungi

Plant-soil feedbacks are a key driver of species diversity and composition in plant communities worldwide; however, the factors that may cause feedbacks to vary within species are rarely examined. In dioecious species, the strength of feedbacks may differ near female plants that produce seed versus near male plants (which do not) because repeated inputs of seeds and high seedling densities near females may cause accumulation of host-specific soil microbes that influence seedling performance. To test whether conspecific seedling performance is reduced near seed-producing female trees relative to male or heterospecific trees, we conducted shadehouse and field experiments with a dioecious tropical tree species, Virola surinamensis (Myristicaceae), on Barro Colorado Island, Panama. The shadehouse experiment isolated the effect of soil microbial communities on seedling growth and allowed us to quantify colonization by mutualistic arbuscular mycorrhizal (AM) fungi, while the field experiment allowed us to assess seedling survival and growth in the presence of nearby conspecific adults and seedlings. In both experiments, seedling performance was similar between seedlings grown in the soil microbial communities and field environments underneath female conspecific, male conspecific, and heterospecific trees. However, contrary to expectation, seedling colonization by AM fungi was higher in male conspecific soil microbial communities than in female or heterospecific soil microbial communities at the end of the shadehouse experiment. Together, our experiments show that while differences among female and male plants in dioecious species may influence the association of conspecific seedlings with AM fungi in their soils, this variation does not necessarily translate directly to differences in seedling performance, at least over the time frame of our experiments. Studies of additional dioecious species are needed to help determine differences in soil microbial communities beneath male and female plants and to assess the role of seed input versus adult root systems in driving plant-soil feedbacks.

ecology↗

bioRxiv2022

Treatment of prostate cancer with CD46 targeted 225Ac alpha particle radioimmunotherapy

Radiopharmaceutical therapy is changing the standard of care in prostate cancer (PCa) and other malignancies. We previously reported high CD46 expression in PCa and developed an antibody-drug conjugate and immunoPET agent based on the YS5 antibody, which targets a tumor-selective CD46 epitope. Here, we present the preparation, preclinical efficacy, and toxicity evaluation of [225Ac]DOTA-YS5, a radioimmunotherapy agent based on the YS5 antibody. Our radiolabeled antibody retains binding efficacy and shows a high tumor to background ratio in PCa xenografts. Furthermore, we show that radiolabeled antibody was able to suppress the growth of cell-derived and patient-derived xenografts, including PSMA-positive and deficient models. Nephrotoxicity, not seen at low radioactive doses, is evident at higher radioactivity dose levels, likely due to redistribution of daughter isotope 213Bi. Overall, this preclinical study confirms that [225Ac]DOTA-YS5 is a highly effective treatment and suggests feasibility for clinical translation of CD46 targeted radioligand therapy in PCa.

cancer biology↗

bioRxiv2020

Cyclic gallium-68 labeled peptides for specific detection of human angiotensin-converting enzyme 2

In this study, we developed ACE2-specific, peptide-derived 68Ga-labeled radiotracers, motivated by the hypotheses that (1) ACE2 is an important determinant of SARS-CoV-2 susceptibility, and (2) that modulation of ACE2 in COVID-19 drives severe organ injury. MethodsA series of NOTA-conjugated peptides derived from the known ACE2 inhibitor DX600 were synthesized, with variable linker identity. Since DX600 bears two cystine residues, both linear and cyclic peptides were studied. An ACE2 inhibition assay was used to identify lead compounds, which were labeled with 68Ga to generate peptide radiotracers ([68Ga]NOTA-PEP). The aminocaproate-derived radiotracer [68Ga]NOTA-PEP4 was subsequently studied in a humanized ACE2 (hACE2) transgenic model. ResultsCyclic DX-600 derived peptides had markedly lower IC50s than their linear counterparts. The three cyclic peptides with triglycine, aminocaproate, and polyethylene glycol linkers had calculated IC50s similar to, or lower than the parent DX600 molecule. Peptides were readily labeled with 68Ga, and the biodistribution of [68Ga]NOTA-PEP4 was determined in a hACE2 transgenic murine cohort. Pharmacologic concentrations of co-administered NOTA-PEP ("blocking") showed significant reduction of [68Ga]NOTA-PEP4 signals in the in the heart, liver, lungs, and small intestine. Ex vivo hACE2 activity in these organs was confirmed as a correlate to in vivo results. ConclusionsNOTA-conjugated, cyclic peptides derived from the known ACE2 inhibitor DX600 retain their activity when N-conjugated for 68Ga chelation. In vivo studies in a transgenic hACE2 murine model using the lead tracer [68Ga]NOTA-PEP4 showed specific binding in the heart, liver, lungs and intestine - organs known to be affected in SARS-CoV-2 infection. These results suggest that [68Ga]NOTA-PEP4 could be used to detect organ-specific suppression of ACE2 in SARS-CoV-2 infected murine models and COVID-19 patients. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/412809v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@f3047org.highwire.dtl.DTLVardef@12ab9a9org.highwire.dtl.DTLVardef@33f43org.highwire.dtl.DTLVardef@12e77ed_HPS_FORMAT_FIGEXP M_FIG For Table of Contents use only C_FIG

biochemistry↗

bioRxiv2018

A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing

Recent studies have reported that CRISPR-Cas9 gene editing induces a p53-dependent DNA damage response in primary cells, which may select for cells with oncogenic p53 mutations11,12. It is unclear whether these CRISPR-induced changes are applicable to different cell types, and whether CRISPR gene editing may select for other oncogenic mutations. Addressing these questions, we analyzed genome-wide CRISPR and RNAi screens to systematically chart the mutation selection potential of CRISPR knockouts across the whole exome. Our analysis suggests that CRISPR gene editing can select for mutants of KRAS and VHL, at a level comparable to that reported for p53. These predictions were further validated in a genome-wide manner by analyzing independent CRISPR screens and patients tumor data. Finally, we performed a new set of pooled and arrayed CRISPR screens to evaluate the competition between CRISPR-edited isogenic p53 WT and mutant cell lines, which further validated our predictions. In summary, our study systematically charts and points to the potential selection of specific cancer driver mutations during CRISPR-Cas9 gene editing.

cancer biology↗