Biology subjects

Simmons, C. R.

Publications and source records attributed to Simmons, C. R..

4 recordsLinked to original sources

bioRxiv2025

Greater Expression of DNA Repair Pathways in Sharks vs. Rays/Skates Based on Transcriptomic Analyses

Elasmobranchs are an understudied taxon of cartilaginous fishes. DNA repair studies have been performed in very few elasmobranchs. Because DNA repair maintains the integrity of the genetic code, it is important for the survival of elasmobranchs in increasingly polluted oceans. Oil spills, for example, have been shown to cause DNA adducts in marine animals. We hypothesized that four elasmobranch species would show differential DNA repair expression. Dermal tissue was harvested from nurse sharks (Ginglymostoma cirratum), spiny dogfish (also considered to be sharks) (Squalus acanthias), yellow stingrays (Urobatis jamaicensis), little skates (Leucoraja erinacea), and RNA was isolated. RNA sequencing was performed using the holocephalan Australian ghostshark (Callorhincus milii) reference genome. ANOVA KEGG pathway analysis revealed that RNA from the sharks manifested significantly higher expression than those of rays/skates in 4/5 major DNA repair pathways (Base Excision, Nucleotide Excision, Mismatch Repair, and Homologous Recombination). Each of the four pathways of DNA repair manifested differential expression of pathway-specific genes (mpg, polL, parp4, polD2, xpa, gtf2h3, gtf2h5, ercc8, ercc4, cul4b, rad51D, rad51C, blm, ssbp1, top3a, rad51, xrcc3, mre11a, brip1, rad54b, etc.). One gene, polD2, was consistently elevated in the sharks vs. rays/skates in all four pathways. A subunit of polD, has been proposed to contribute to the spreading and amplification of hypermutations in sharks by generating higher diversity of the T cell receptor repertoire. With increased expression of four major DNA repair pathways, sharks may be more successful than rays/skates in remediating DNA damage and surviving the genotoxic effects of increasingly polluted oceans and possibly eluding cancer.

molecular biology↗

bioRxiv2024

Cancer-Specific Alterations in Nuclear Matrix Proteins Determined by Multi-omics Analyses of Ductal Carcinoma in Situ

Breast cancer (BC) is the most common cancer affecting women in the United States. Ductal carcinoma in situ (DCIS) is the earliest identifiable pre-invasive BC lesion. Estimates show that 14 to 50% of DCIS cases progress to invasive BC. Our objective was to identify nuclear matrix proteins (NMP) with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast reduction mammoplasty and a contralateral breast explant using mass spectrometry and RNA sequencing to accurately identify aggressive DCIS. Sixty NMPs were significantly differentially expressed between the DCIS and non-diseased breast epithelium in an isogenic contralateral pair of patient-derived extended explants. Ten of the sixty showed significant mRNA expression level differences that matched the protein expression. These 10 proteins were similarly expressed in non-diseased breast reduction cells. Three NMPs (RPL7A, RPL11, RPL31) were significantly upregulated in DCIS and all other BC stages compared to the matching contralateral breast culture and an unrelated non-diseased breast reduction culture. RNA sequencing analyses showed that these three genes were upregulated increasingly with BC progression. Finally, we identified three NMPs (AHNAK, CDC37 and DNAJB1) that were significantly downregulated in DCIS and all other BC stages compared to the isogenically matched contralateral culture and the non-diseased breast reduction culture using both proteomics and RNA sequencing techniques.

cancer biology↗

bioRxiv2023

Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals

The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven elusive since its conception. Oligonucleotide frameworks provide an especially attractive route towards studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via x-ray crystallography, as a proof-of-principle towards scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an anti-parallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.

bioengineering↗

bioRxiv2021

Structural origins of altered spectroscopic properties upon ligand binding in proteins containing a fluorescent non-canonical amino acid.

Fluorescent non-canonical amino acids (fNCAAs) could serve as starting points for the rational design of protein-based fluorescent sensors of biological activity. However, efforts toward this goal are likely hampered by a lack of atomic-level characterization of fNCAAs within proteins. Here, we describe the spectroscopic and structural characterization of five streptavidin mutants that contain the fNCAA L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) at sites proximal to the binding site of its substrate, biotin. Many of the mutants exhibited altered fluorescence spectra in response to biotin binding, which included both increases and decreases in fluorescence intensity as well as red or blue shifted emission maxima. Structural data were also obtained for three of the five mutants. The crystal structures shed light on interactions between 7-HCAA and functional groups--contributed either by the protein or substrate--that may be responsible for the observed changes in the 7-HCAA spectra. These data could be used in future studies aimed at the rational design of fluorescent, protein-based sensors of small molecule binding or dissociation.

biochemistry↗