Biology subjects

Beckmann, K.

Publications and source records attributed to Beckmann, K..

4 recordsLinked to original sources

bioRxiv2023

GxE PRS: Genotype-environment interaction in polygenic risk score models for quantitative and binary traits

The use of polygenic risk score (PRS) models has transformed the field of genetics by enabling the prediction of complex traits and diseases based on an individuals genetic profile. However, the impact of genotype-environment interaction (GxE) on the performance and applicability of PRS models remains a crucial aspect to be explored. Currently, existing GxE PRS models are often inappropriately used, which can result in inflated type 1 error rates and compromised results. In this study, we propose a novel GxE PRS model that correctly incorporates the GxE component to analyze complex traits and diseases. Through extensive simulations, we demonstrate that our proposed model outperforms existing models in terms of controlling type 1 error rates and enhancing statistical power. Furthermore, we apply the proposed model to real data, and report significant GxE effects. Specifically, we highlight the impact of our model on both quantitative and binary traits. For quantitative traits, we uncover the GxE modulation of genetic effects on body mass index (BMI) by alcohol intake frequency (ALC). In the case of binary traits, we identify the GxE modulation of genetic effects on hypertension (HYP) by waist-to-hip ratio (WHR). These findings underscore the importance of employing a robust model that effectively controls type 1 error rates, thus preventing the occurrence of spurious GxE signals. To facilitate the implementation of our approach, we have developed an innovative R software package called GxE PRS, specifically designed to detect and estimate GxE effects. Overall, our study highlights the importance of accurate GxE modeling and its implications for genetic risk prediction, while providing a practical tool to support further research in this area.

genetics↗

bioRxiv2023

Fcgamma-receptor-independent controlled activation of CD40 canonical signaling by novel therpeutic antibodies for cancer therapy

Activation of CD40-mediated signaling in antigen-presenting cells is a promising therapeutic strategy to promote immune responses against tumors. Agonistic anti-CD40 antibodies currently in development require Fc{gamma}-receptor-mediated crosslinking of CD40 molecules for meaningful activation of CD40 signaling but have limitations due to dose-limiting toxicities. Here we describe the identification of CD40 antibodies which strongly stimulate antigen-presenting cells in an entirely Fc-independent manner. These novel Fc-silenced anti-CD40 antibodies induce upregulation of costimulatory receptors CD80 and CD86 and cytokine release by dendritic cells with an efficacy exceeding that of existing antibodies. Binding to the CD40L interaction region on CD40 appears to be a prerequisite to achieving such strong activities. Finally, the most active identified anti-CD40 antibody shows evidence of activity in terms of the expected markers of canonical CD40 signaling when injected in humanized mice. There are no signs of obvious toxicities whereas the clinical-stage anti-CD40 antibody CP-870,893 induced severe signs of toxicity in these animals despite a lower dose compared with the novel Fc-silenced canonical agonist. These studies thus demonstrate potent activation of antigen-presenting cells with anti-CD40 antibodies lacking Fc{gamma}-receptor-binding activity and open the possibility of an efficacious and safe combination therapy for cancer patients. One Sentence SummaryTreatment of antigen-presenting cells and humanized mice with novel Fc-silenced CD40 antibodies demonstrates an Fc{gamma}-receptor-independent canonical agonistic mode of action for therapeutic use.

immunology↗

bioRxiv2022

Direct access to millions of mutations by Whole Genome Sequencing of an oilseed rape mutant population

Induced mutations are an essential source of genetic variation in plant breeding. EMS mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In this study, a rapeseed M2 population was derived from M1 parent cultivar "Express" treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1,988 M2 plants representing 497 M2 families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284,442 single nucleotide polymorphisms per M2 DNA pool were found resulting from EMS mutagenesis. 55% were C[->]T and G[->]A transitions, characteristic for EMS induced ( canonical) mutations, whereas the remaining SNPs were non-canonical transitions (15%) or transversions (30%). Additionally, we detected 88,725 high confidence insertions and deletions (InDels) per pool. On average, each M2 plant carried 39,120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Roughly 82% of such mutations were located either 5 kb upstream or downstream (~56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole-genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool "EMS Brassica" (http://www.emsbrassica.plantbreeding.uni-kiel.de/), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.

genomics↗

bioRxiv2022

Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus

Rapeseed (Brassica napus L.) is an important oil crop and harbours the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has a high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction of seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping-by-sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant correlation with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.

genomics↗