Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the laboratory as in nature. The base-substitution spectrum differs between C. elegans laboratory mutation accumulation (MA) experiments and the standing site-frequency spectrum, which has been argued to be in part owing to increased oxidative stress in the laboratory environment. Using genome sequence data from C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased oxidative stress, we find the base-substitution spectrum is similar between mev-1, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). Conversely, the rate of short insertions is greater in mev-1, consistent with studies in other organisms in which environmental stress increased the rate of insertion–deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are different from those of nonmononucleotide sequence, both for indels and base-substitutions, and whereas the nonmononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different, with a greater frequency of A:T → T:A transversions and an increased proportion of ±1-bp indels. The discrepancy in mutational spectra between laboratory MA experiments and natural variation is likely owing to a consistent (but unknown) effect of the laboratory environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.

Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the lab as in nature. The ratio of transitions to transversions (Ts/Tv) is consistently lower in C. elegans mutation accumulation (MA) experiments than in nature, which has been argued to be in part due to increased oxidative stress in the lab environment. Using whole-genome sequence data from a set of C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased endogenous oxidative stress, we find that the base-substitution spectrum is similar between mev-1 lines, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). By contrast, the rate of short insertions is greater in the mev-1 lines, consistent with studies in other organisms in which environmental stress led to an increase in the rate of insertion-deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are qualitatively different from those of non-mononucleotide sequence, both for indels and base-substitutions, and whereas the non-mononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different. The discrepancy in mutational spectra between lab MA experiments and natural variation is likely due to a consistent (but unknown) effect of the lab environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.

Caenorhabditis elegans strains with the heat-sensitive mortal germline phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans’ tolerance. Mortal germline is transgenerationally heritable, and proximately under epigenetic control. Previous studies have suggested that mortal germline presents a relatively large mutational target and that mortal germline is not uncommon in natural populations of C. elegans. The mortal germline phenotype is not monolithic. Some strains exhibit a strong mortal germline phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the mortal germline phenotype and (2) quantify the frequency of mortal germline in a collection of 95 wild isolates. Over the course of ∼16,000 meioses, we detected one mutation to a strong mortal germline phenotype, resulting in a point estimate of the mutation rate UMrt≈ 6 × 10−5/genome/generation. We detected no mutations to a weak mortal germline phenotype. Six out of 95 wild isolates have a strong mortal germline phenotype, and although quantification of the weak mortal germline phenotype is inexact, the weak mortal germline phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong mortal germline phenotype s¯≈0.1%, similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak mortal germline variants in nature combined with the low mutation rate suggests that mortal germline may be maintained by balancing selection.

C. elegans strains with the mortal germline (Mrt) phenotype become progressively sterile over the course of a few tens of generations. Mrt is proximately controlled epigenetically, and is typically temperature-dependent, being penetrant at temperatures near the upper range of C. elegans’ tolerance. Previous studies have suggested that Mrt presents a relatively large mutational target, and that Mrt is not uncommon in natural populations of C. elegans. The Mrt phenotype is not monolithic. Some strains exhibit a strong Mrt phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the Mrt phenotype, and (2) quantify the frequency of Mrt in a collection of 95 wild isolates. Over the course of ~16,000 meioses, we detected one mutation to a strong Mrt phenotype, resulting in a point estimate of the mutation rate ⋃Mrt≈ 6×10−5/genome/generation. We detected no mutations to a weak Mrt phenotype. 5/95 wild isolates had a strong Mrt phenotype, and although quantification of the weak Mrt phenotype is inexact, the weak Mrt phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong Mrt phenotype , similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak Mrt variants in nature combined with the low mutation rate suggests that Mrt may be maintained by balancing selection.

Even after radiation treatment, prostate cancer (PCa) patients receiving radiotherapy (RT) are still at risk for disease progression and recurrence. Predicting outcomes associated with cancer treatment is critical to PCa survivorship given that the 5-year survival rates for local and regional stage PCa is nearly 100%. Radiogenomics is a promising field of research focused on identifying genomic markers that can provide clinically useful prognostic predictions regarding radiation response and can potentially serve as the basis for personalized RT where cancer management is tailored to fit each individual patient. Circulating cell-free (ccfDNA) DNA has been found to 1) be associated with radiation sensitivity or toxicity, 2) relapse or recurrence, and 3) risk for the development of metastases before, during or following photon RT. Proton therapy, alternative to photon therapy, is a promising treatment that can reduce excess radiation dose and, in turn, the risk for adverse events. However, few studies have been done to determine if ccfDNA can predict response in proton radiation, which purports superior dose distribution, avoiding healthy tissues, minimizing the exit dose, and potentially reducing overall toxicity. The overall aim of this study is to determine if the quantity of ccfDNA is associated with PCa risk groups. We hypothesized that PCa patients within the highest risk group have quantitatively increased levels of ccfDNA compared to those in low and intermediate risk groups. This study leveraged the University of Florida Health Proton Therapy Institute Outcomes Tracking Protocol biobank of PCa patients with plasma and serum collected before, during and after proton RT. Isolation of ccfDNA at baseline, during treatment, and following treatment was undertaken and ccfDNA quantities were compared among patients in the low, intermediate and high risk groups using ANOVA. Our results indicate that the quantity difference between baseline and day 14 of treatment (p=0.055), 2 weeks post-treatment (p=0.54), and 4 weeks post-treatment (p=0.002) was associated with risk group. There was trend towards increasing ccfDNA quantity, as risk group increased; however, there was no correlation between risk group and treatment times using the Pearson correlation. Our results were consistent in that high ccfDNA quantity was associated with PCa risk. This is the first study determining the application of ccfDNA quantity on prostate cancer outcomes in patients undergoing proton RT. Identifying the determinants of radiation-related adverse outcomes will help inform impending predictive genomic technologies and improve cancer-related outcomes and survivorship. Citation Format: Andrew Bass, Johnny Velasquez, Moein Rajaei, Curtis Bryant, Nancy Mendenhall, Luisel J. Ricks-Santi. Association of circulating cell-free DNA and prostate cancer risk groups in patients undergoing proton therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5594.