Biology subjects

Rorex, C.

Publications and source records attributed to Rorex, C..

4 recordsLinked to original sources

bioRxiv2026

CODMA-A3: A Competitive Oligo-based DNA Modification Assay Applied to APOBEC Enzymes

Quantifying the functional effects of human variation in proteins is a challenge because bioinformatic pipelines allow variant detection to outpace experimental characterization. This results in a practical problem of resource allocation to identify the most scientifically significant variants to prioritize for mechanistic investigation. There are many approaches appropriate depending on class of enzymatic activity being investigated. However, fundamental to many of these approaches is a trade-off between mechanistic insight and throughput. In seeking to understand how activity changes across human variants of the APOBEC3 family of proteins we sought to create an early screening assay to prioritize variants for mechanistic study. We wanted an assay that was not dependent on protein purification, allowed for multiple-substrate competition and could be executed in a microtiter plate allowing for high throughput and approximate normalized substrate turnover without requiring classic Michaelis-Menten approaches. Here we describe CODMA (Competitive Oligo-based DNA Modification Assay) and applied it to A3 enzymology as a method to rapidly screen A3 constructs for changes in substrate utilization fingerprints. CODMA-A3 detected effects of substrate competition, distinguished fluorophore identity from substrate sequence effects, resolved activity changes caused by a single nucleotide substitution within a competing substrate, and identified shifts in substrate utilization following modification of lysate composition, oligonucleotide architecture, or antibody-mediated protein perturbation. CODMA-A3 occupies a methodological niche between low-throughput mechanistic assays and sequencing-intensive approaches by providing a rapid, inexpensive screening platform for comparative characterization of 20 to 40 enzyme variants prior to detailed mechanistic investigation.

biochemistry↗

bioRxiv2026

Deciphering the Network Architecture of APOBEC3-Driven Mutagenesis in HPV-Positive Head and Neck Cancers

APOBEC3A (A3A) and APOBEC3B (A3B) are cytosine deaminases that restrict viral infection and can also mutate the host genome. In human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSCC), expression of both enzymes is elevated, but bulk sequencing averages their effects across mixed cell populations. Here we profile single cells from HPV16-positive HNSCC tumors and matched normal tissue. We find that the APOBEC3 (A3) single base substitution mutational signature, SBS2, is enriched in cells expressing more A3A than A3B, whereas copy number alteration (CNA) burden is enriched in cells expressing more A3B than A3A. Tumor versus normal co-expression networks identify the A3 interactors RALY and HNRNPA2B1 as candidate A3 activators. We found that SBS2 and CNA mark the maintenance and productive stages of HPV16 lifecycle, and their ratio may offer a molecular estimate of tumor age. The neoantigens from immune-visible SBS2-HIGH and immune-evasive CNA-HIGH cells identify candidates for mRNA vaccines matched to a tumor's viral state.

cancer biology↗

bioRxiv2026

APOBEC3G Splicing Defects in Nonhuman Primate Models Result in Disparate Viral Mutational Profiles Relative to Humans

Nonhuman primates (NHPs), particularly macaques, are indispensable models for studying human infectious diseases due to their close immunological and physiological similarities. Understanding species-specific molecular differences is essential for maximizing the translational value of these models. Here we report that APOBEC3G (A3G), a potent antiviral restriction factor and the major source of genetic variations in HIV, exhibits a widespread mRNA splicing defect in the Cercopithecinae subfamily, which includes the commonly used NHP models. Driven by intronic polymorphisms, this splicing defect substantially reduces A3G protein levels and consequently results in a markedly reduced A3G-mediated mutation signatures, fewer defective viral genomes, and greater viral diversification in SIV compared to HIV. This species-specific effect is not restricted to lentiviruses: reduced A3G signatures have also been reported in simian foamy virus and simian T-cell leukemia virus, suggesting broader effects across primate retroviruses. These findings reveal a lineage-specific alteration in a major antiviral restriction factor, with important implications for viral restriction, evolution, drug resistance, and immune evasion. They also highlight the importance of incorporating naturally occurring genetic variation into NHP model selection to improve the reproducibility, translational fidelity, and biological relevance of preclinical research.

genomics↗

bioRxiv2019

Changes in the microbial community of Lubomirskia baicalensis affected by Brown Rot Disease

Sponge diseases occur globally and the resulting reduction of sponge populations has negative effects on other organisms within the ecosystems due to loss of nutrient enrichment and loss of bioremediation. In Lake Baikal, the predominate sponge species Lubomirskia baicalensis is currently being infected with an unidentified pathogen resulting in a sharp decline in population. The current hypothesis is that the recent increase in methane concentration in the lake has caused dysbiosis within the bacterial community of L. baicalensis resulting in the disease outbreak. In this study we investigated the changes in the bacterial community between healthy and sick sponges using 16S bacterial profiling targeting veritable regions 3-5. Here we present data that the bacterial communities of the healthy sponge samples were significantly different from sick samples and several poorly classified organisms were identified by Indicator Species Analysis as significant. Organisms identified from the sick samples classified within taxonomic units that contain acidophilic bacteria which suggest pH may play a role. There was also an observed decrease in the number of identified methyltropic bacteria present in the sick sponge samples compared to the healthy.

ecology↗